Change color gradient plot functions
 

 bug-fix: miss-match rows for n_print
 

 bug-fix: integer overflow in onc * onr
 

 Fix doi citation issue from reviewer's suggestion
 

 version bump
 

 Add inverse rank normalisation (invnorm) to transformAssay (#766)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: Tuomas Borman <tvborm@utu.fi> 

 pseudocount message (#776)

Signed-off-by: Daena Rys <rysdaena8@gmail.com> 

 Minor modification to addAlpha documentation (#778)

Signed-off-by: Daena Rys <rysdaena8@gmail.com> 

 Adding difference and division (#740)

Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: Tuomas Borman <tvborm@utu.fi> 

 Fix test-mediate.R (#750)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 MetaboDynamics 1.6: new functions added: see NEWS
 

 re-run of example data needed
 

 altered vignette for dataframes
 

 bug fixes
 

 bug fix
 

 bug fix
 

 abstract to top
 

 styling and bug fixes
 

 new example data with clustering and ORA results on two conditions
 

 bug fix
 

 bug fix
 

 bug fixes
 

 binding of global variables and check bug fixes
 

 bug fixes
 

 bug fix
 

 bug fixes
 

 added ORA analysis for faster examples and easier vignette
 

 plot_ORA tests
 

 plot_ORA suitable for patchwork
 

 adapted plot_ORA
 

 bug fixes
 

 updated readme questions
 

 tests plot_cluster
 

 added question
 

 typo
 

 cluster order added
 

 matching lineplot to cluster ID and bubbletree
 

 bug fix
 

 bug fixes on cluster_dynamics
 

 example fixed
 

 cluster_dynamics with bootstraps from mu posterior
 

 draft cluster dynamics with bootstrapping
 

 move helper functions all in "utils"
 

 bug fixes
 

 adapted estimates_dynamics function
 

 added model choice to examples
 

 documentation of plot_PPC
 

 adapted example in plot_diagnostics
 

 adapted fit_dynamics function: runs on all conditions in parallel (needed for euclidean distance) and has the option for fitting raw metabolite abundances + cell counts
 

 revise document of plot-AAspectra
 

 revise document of plotAAspectra.R and plotProteinSipPct.R
 

 Stop tracking .vscode
 

 change tests using built-in demo files
 

 update Aerith.Rmd, Input-data-format.Rmd, PSM-annotation-and-visualization.Rmd. Remove eval=FALSE chunks
 

 Merge branch 'main' into dev
 

 igblastr 0.99.17: Perl is no longer a system requirement

Only reason Perl was needed was because we were using Perl
script 'edit_imgt_file.pl' (distributed with IgBLAST) to clean
IMGT FASTA files. This step is now implemented in R in internal
helper redit_imgt_file().
 

 Merge branch 'devel' of git.bioconductor.org:packages/tximeta into devel
 

 GENCODE 49 (H.s.), M38 (M.m), and Ensembl 115
 

 bump gha cache
 

 Added returnData argument to plotFoldChange
 

 mark unit test invalidSmileParsing as requireing chemmineob
 

 bumpt, added biocview
 

 Stabilize tests with tolerance; bump to 1.19.2
 

 Bump version
 

 Remove commented-out code related to Matrix.utils in collapseMutants
 

 feat: add additional replacement methods

- Add `mz<-` and `intensity<-` methods.
 

 - added doi entry to CITATION file
- bumped version to 0.99.2
 

 missMethyl 1.43.1: Add GenomeInfoDb to Imports
 

 Update to the latest umappp, enable the previously-commented options.
 

 Updated t-SNE bindings to allow the user to specify lesser-used options.
 

 Added a separate function to compute block weights.

This mostly aims to provide a central location for documenting the weighting
scheme, but others could use it to define weights for their own calculations.
 

 bump up version and add to news
 

 [skip actions] Bump version to 1.7.2.9008
 

 [skip actions] Bump version to 1.7.2.9007
 

 [skip ci] Update WORDLIST
 

 Do not use `testthat` dependent features in the app (#237)

`teal.gallery` [e2e
tests](https://github.com/insightsengineering/teal.gallery/actions/runs/16713540730/job/47302517585)
caught an error that originates here. If `testthat` package is not
installed when running the app it throw an error in the app.
```
Warning: Error in makeExpectation: Package 'testthat' is required for checkmate's 'expect_*' extensions with backend 'testthat'
  195: stop
  194: makeExpectation [/tmp/RtmpCWBQUh/renv-package-new-52d51bba257/checkmate/R/makeExpectation.R#80]
  193: expect_proportion [/__w/teal.gallery/teal.gallery/RNA-seq/renv/staging/1/hermes#1]
  192: hermes::control_quality [/tmp/RtmpCWBQUh/renv-package-new-52d7cce5949/hermes/R/quality.R#39]
  191:  [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#300]
  171: control [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  170:  [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#309]
  150: object_flagged [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  149:  [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#325]
  129: object_final [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  128:  [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#346]
  108: plot_r [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  101: renderUI [/tmp/RtmpCWBQUh/renv-package-new-52d60693a47/teal.widgets/R/plot_with_settings.R#407]
  100: func [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/utils.R#1482]
   87: renderFunc [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/shinywrappers.R#263]
   86: output$teal-teal_modules-nav-quality_control-module-plot-plot_out_main [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/shinywrappers.R#133]
    1: shiny::runApp [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/runapp.R#388]
    1) Navigates to all tabs without error
```

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> </pre>
    </div>
  
    

      Package: hermes

      Commit: aa791929b6d00d52beb047cb993920554f20227a

      Author:  m7pr <133694481+m7pr@users.noreply.github.com> 

      Date: 2025-01-24 15:00:25 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.2.9005
 
    
  
    

      Package: hermes

      Commit: cd56c7aa1080ad61f2c0b6c9208551eb30e84a54

      Author:  Marcin <133694481+m7pr@users.noreply.github.com> 

      Date: 2025-01-24 15:59:33 +0100

      Commit message:


	  
		
 Fix Scheduled job (#234)

WIP
https://github.com/insightsengineering/hermes/actions/runs/12888089889

---------

Co-authored-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com> 
    
  
    

      Package: hermes

      Commit: acd1bf0c10a48975607e1cca8d999bb219efe40f

      Author:  vedhav <vedhav@users.noreply.github.com> 

      Date: 2024-12-12 14:34:02 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.2.9004
 
    
  
    

      Package: hermes

      Commit: 5d72b382fb1473917a57270e412dcd7b23fcf430

      Author:  Vedha Viyash <49812166+vedhav@users.noreply.github.com> 

      Date: 2024-12-12 20:03:08 +0530

      Commit message:


	  
		
 add setup-r-dependencies (#233)

Related to
https://github.com/insightsengineering/nestdevs-tasks/issues/65
Switch to setup-r-dependencies.
Added `hermes` for lookup-refs. 
    
  
    

      Package: hermes

      Commit: e7eb4b4ef6393bd5d64e89fb9dc6111b33ca0f02

      Author:  walkowif <walkowif@users.noreply.github.com> 

      Date: 2024-09-16 07:03:27 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.2.9003
 
    
  
    

      Package: hermes

      Commit: 2204c59b329c7edc4f2973dceca536aa0d810841

      Author:  walkowif <59475134+walkowif@users.noreply.github.com> 

      Date: 2024-09-16 09:02:30 +0200

      Commit message:


	  
		
 Workflow propagations (#232)

 
    
  
    

      Package: hermes

      Commit: 9cd9472f80f119c49f887fe5c27a826b17fa844a

      Author:  cicdguy <cicdguy@users.noreply.github.com> 

      Date: 2024-08-22 11:35:07 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.2.9002
 
    
  
    

      Package: hermes

      Commit: 7dad0b50aac06ec91d7739724a58a532e7f4d9bc

      Author:  walkowif <59475134+walkowif@users.noreply.github.com> 

      Date: 2024-08-22 13:34:09 +0200

      Commit message:


	  
		
 Workflow propagations (#231)

Propagation of:
* https://github.com/insightsengineering/idr-tasks/issues/781
* https://github.com/insightsengineering/idr-tasks/issues/785
* https://github.com/insightsengineering/idr-tasks/issues/793
* https://github.com/insightsengineering/idr-tasks/issues/800
* https://github.com/insightsengineering/idr-tasks/issues/802 
    
  
    

      Package: hermes

      Commit: 11e90924a4c215a01d15cd314df3a110decdd299

      Author:  BFalquet <BFalquet@users.noreply.github.com> 

      Date: 2024-07-16 16:21:05 +0000

      Commit message:


	  
		
 [skip ci] Update WORDLIST
 
    
  
    

      Package: hermes

      Commit: f5c75084a1d3719b5e90cc8ad856daf9acebb874

      Author:  BFalquet <BFalquet@users.noreply.github.com> 

      Date: 2024-07-16 16:20:10 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.2.9001
 
    
  
    

      Package: hermes

      Commit: ada9a4fcdd1828c799579dc81d7a4028fe6510d3

      Author:  b_falquet <64274616+BFalquet@users.noreply.github.com> 

      Date: 2024-07-16 18:19:18 +0200

      Commit message:


	  
		
 fix integration tests (#230)

- fix integration test by testing the undelying data frame rather than
the plot.
- switch to 3rd edition of testthat

thank you for the review 
    
  
    

      Package: hermes

      Commit: dbe50ae04ac3e0f5a2069753c997f5de77e6f3c1

      Author:  danielinteractive <danielinteractive@users.noreply.github.com> 

      Date: 2024-06-27 13:59:44 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.2.9000
 
    
  
    

      Package: hermes

      Commit: fdf4ec82e3643e6a632b2cb29b1db6ae7943e434

      Author:  Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> 

      Date: 2024-06-27 15:58:37 +0200

      Commit message:


	  
		
 change email (#229)

part of #228
 
    
  
    

      Package: hermes

      Commit: b5b6fd0f4d3ff3e444c332630360bdd1b94de00b

      Author:  cicdguy <cicdguy@users.noreply.github.com> 

      Date: 2024-04-29 15:55:00 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.1.9002
 
    
  
    

      Package: hermes

      Commit: 1fe87681f8e29c91ce5cadb89abd373d7f69b6fe

      Author:  walkowif <59475134+walkowif@users.noreply.github.com> 

      Date: 2024-04-29 17:53:57 +0200

      Commit message:


	  
		
 Workflow propagation (#226)

Propagation of:
* https://github.com/insightsengineering/idr-tasks/issues/355
* https://github.com/insightsengineering/idr-tasks/issues/756
* https://github.com/insightsengineering/idr-tasks/issues/757
* https://github.com/insightsengineering/idr-tasks/issues/712
* https://github.com/insightsengineering/idr-tasks/issues/764 
    
  
    

      Package: hermes

      Commit: ab4e8adf0ea74e0f818fe4aba72d4748948274f0

      Author:  danielinteractive <danielinteractive@users.noreply.github.com> 

      Date: 2024-03-06 21:07:07 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.1.9001
 
    
  
    

      Package: hermes

      Commit: dbe789ecc324235f13bc5b32bd1e222f036f7ddc

      Author:  Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> 

      Date: 2024-03-06 22:06:03 +0100

      Commit message:


	  
		
 update snapshots, fix typo (#225)

closes #224 
    
  
    

      Package: hermes

      Commit: 0aea21d8660eca06fe930096e9c9c24fa5f60da6

      Author:  danielinteractive <danielinteractive@users.noreply.github.com> 

      Date: 2024-02-13 20:51:55 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.7.1.9000
 
    
  
    

      Package: hermes

      Commit: 5b0ca967fee1c49dccf6f9aba2905c85a9f9c323

      Author:  Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> 

      Date: 2024-02-13 21:50:55 +0100

      Commit message:


	  
		
 release 1.7.1 to sync with BioC (#223)

closes #203 
    
  
    

      Package: hermes

      Commit: 18db786faca3790931b43a6929a83380cb241466

      Author:  danielinteractive <danielinteractive@users.noreply.github.com> 

      Date: 2024-02-13 20:14:04 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.0.1.9023
 
    
  
    

      Package: hermes

      Commit: 52c5614ce4e98c4322738047986c07e25958d290

      Author:  Vedha Viyash <49812166+vedhav@users.noreply.github.com> 

      Date: 2024-02-14 01:43:06 +0530

      Commit message:


	  
		
 Fix pkgdown redirect (#221)

Part of https://github.com/insightsengineering/coredev-tasks/issues/506

---------

Signed-off-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> 
    
  
    

      Package: hermes

      Commit: 51667507f4b49f02f747e230c5c41642dbdae8ac

      Author:  danielinteractive <danielinteractive@users.noreply.github.com> 

      Date: 2024-02-13 10:41:02 +0000

      Commit message:


	  
		
 [skip actions] Bump version to 1.0.1.9022
 
    
  
    

      Package: hermes

      Commit: 775f43b4f52461986e941e730d71ca5280b49e79

      Author:  b_falquet <64274616+BFalquet@users.noreply.github.com> 

      Date: 2024-02-13 11:40:09 +0100

      Commit message:


	  
		
 220 update snapshots (#222)

https://github.com/insightsengineering/hermes/issues/220

close #220 

thank you for the review

---------

Co-authored-by: benoit <benoit.falquet@roche.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com> 
    
  
    

      Package: notame

      Commit: 6a54d01d68179f564ddd746ad4c74f71630c3128

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-08 17:50:50 +0300

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: notame

      Commit: c200427106eff6377c0c60ad5a839070a18850b4

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-08 17:49:09 +0300

      Commit message:


	  
		
 Cleaning
 
    
  
    

      Package: notame

      Commit: e89a2dacd872eac7c17e2c5c824736d555022538

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-08 11:22:58 +0300

      Commit message:


	  
		
 Revert flag_quality() to use "condition" argument
 
    
  
    

      Package: notame

      Commit: dfa6af9b5592ee6d068c9453fab02be27f3972fd

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-08 11:04:56 +0300

      Commit message:


	  
		
 Revert correct drift and remove plotting

Revert to allow use without creating multiple assays and re-include 
condition argument. Remove "plotting" argument, visualizations can soon 
be plotted separately with notameViz.
 
    
  
    

      Package: notame

      Commit: fe268d102af30d8a0a9d6f0ea3249b68030d4c72

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-02 17:17:25 +0300

      Commit message:


	  
		
 Sync notame packages 1

Outline ok, passes R CMD check, not considered BiocCheck yet.
 
    
  
    

      Package: notame

      Commit: 19c973dd1da7b30ada447f8ffaa0f1dd3a724256

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-02 00:48:53 +0300

      Commit message:


	  
		
 Change example_set to toy_notame_set, same content.
 
    
  
    

      Package: notame

      Commit: dfbf1afefca57f64e812142960e2955fb3c7671d

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-01 18:20:06 +0300

      Commit message:


	  
		
 Change quality metrics to only include dual condition with RSD_r and D_ratio_r in flag_quality() and correct_drift()
 
    
  
    

      Package: notame

      Commit: ef4e85e1af8446ae1ebc0d28efafecbf99e446c0

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-09-01 16:54:38 +0300

      Commit message:


	  
		
 Rename merge objects to merge_notame_sets
 
    
  
    

      Package: notame

      Commit: ec5ba1ce7d221830d9d5e2604de868df3ee52731

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-08-31 21:47:49 +0300

      Commit message:


	  
		
 Modify correct_drift() to use multiple assays and make save_dc_plots() more interoperable. 

save_dc_plots() to be moved to notameViz. Now takes all data from a 
single SE object. correct_drift() at large modified accordingly;  
the predicted values for spline are returned as an assay.
 
    
  
    

      Package: notame

      Commit: 7c1bd81e22a9a50316030b18634f7aaa9d9c8e59

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-08-31 15:57:41 +0300

      Commit message:


	  
		
 Use SE instead of data.frame in visualize_clusters

To be included in notameViz. Removed unfinished graph plot which 
required igraph object to make change feasible. New arguments for 
selecting clustering metadata columns for interoperability.
 
    
  
    

      Package: notame

      Commit: 66676cb060ae4d855755e38f7d3d25090f98e0aa

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-08-30 21:51:35 +0300

      Commit message:


	  
		
 Re-include website (one covers all notame packages) and vignette terminology changes from main branch

Updated custom reference index to account for multiple packages. 
notameViz and notameStats functions reference link to rdrr.io. The 
vignettes can also be included on website without being included in the 
built package.
 
    
  
    

      Package: notame

      Commit: 30ece908dc324c7e3862cee7042385ce248103cd

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-08-30 21:45:44 +0300

      Commit message:


	  
		
 Rename and modify read_from_excel() to import_from_excel()

Returns SummarizedExperiment instead of list with parts
 
    
  
    

      Package: notame

      Commit: e127a6d2b13bfb7081d30d01a855d98932cf24b1

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-08-22 10:46:28 +0300

      Commit message:


	  
		
 Native pipe operator
 
    
  
    

      Package: notame

      Commit: 7cce84a5fd07eece3ea1f65ca39df05abb899b32

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-08-22 09:53:27 +0300

      Commit message:


	  
		
 Initial version after split
 
    
  
    

      Package: notame

      Commit: ce85add8b21428be594f15a1a008557651962a20

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-06-25 10:38:42 +0300

      Commit message:


	  
		
 Remove preprocessing visualizations?

Doing eval = FALSE for vignette at this point as we decide on the scope.
 
    
  
    

      Package: notame

      Commit: 579b90ba22ec9c79aeb235e2f976607d3c59a660

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-06-24 19:29:59 +0300

      Commit message:


	  
		
 Remove stats

Leave perform_lm() for preprocessing visualizations
 
    
  
    

      Package: notame

      Commit: 28ca9b782784b15ee91b5987d2ee435a96d9d257

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-06-21 19:27:05 +0300

      Commit message:


	  
		
 Vignette update: use multiple assays

This is needed as log- and other transformations were removed (because 
we can't add assay.type argument to the generics and transformations are 
highly redundant functionality)
 
    
  
    

      Package: notame

      Commit: c3ab6bd70c558a06f806c26a4852adf5c79e410a

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-06-21 15:35:49 +0300

      Commit message:


	  
		
 Bug fix for fix_object(): keep assay names when splitting object.

Did not include functionality for keeping names of multiple assays, this 
shouldn't be needed at this stage of processing.
 
    
  
    

      Package: notame

      Commit: 7f6679e2e5ad4a5d994d5b39aff3f80abc397231

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-06-19 16:31:20 +0300

      Commit message:


	  
		
 Remove functionality

- multivariate
- results visualizations
 
    
  
    

      Package: notame

      Commit: db0fbb027b0b8498bc9864c0bd45b0411d4bd57a

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-06-18 09:23:13 +0300

      Commit message:


	  
		
 Plain functions instead of methods after removing MetaboSet-support. Completely removed log methods and exponential as it is not possible to add assay.type as new argument to base R generics; we should use multiple assays instead.
 
    
  
    

      Package: notame

      Commit: 07be100420f30c8c0c2da18d2e57704c684a796c

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-06-18 07:55:45 +0300

      Commit message:


	  
		
 Remove MetaboSet-support
 
    
  
    

      Package: notame

      Commit: f4a51d82788f228c559fce40440fc5b40b55b089

      Author:  vsuksi <vsuksi@abo.fi> 

      Date: 2025-05-14 16:38:11 +0300

      Commit message:


	  
		
 Bug fix

In mixomics_plsda_optimize() and mixomics_pls_optimize(), pass all 
parameters needed to build final model.
 
    
  
    

      Package: MDSvis

      Commit: f40b107561a7fca80417b1ca31dc488d4ba8218a

      Author:  phauchamps <philippehauchamps@hotmail.com> 

      Date: 2025-09-08 16:32:13 +0200

      Commit message:


	  
		
 slight tech changes to solve WARNINGS on Bioc building systems
 
    
  
    

      Package: ELViS

      Commit: c2ad00cd5b086a0931cd09bf9709da64db3343b5

      Author:  jlee307@uthsc.edu <jlee307@clr0736.cn.isaac.utk.edu> 

      Date: 2025-09-08 11:02:43 -0400

      Commit message:


	  
		
 added error handling
 
    
  
    

      Package: scRNAseqApp

      Commit: 8563a984ad2d51b7c189e460eba1464d5b43a59d

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-09-08 10:42:41 -0400

      Commit message:


	  
		
 fix a bug for file accessibility check.
 
    
  
    

      Package: scRNAseqApp

      Commit: 7dd9c222dc92172df26cdc7f25cf48519d2786b2

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-09-08 09:42:20 -0400

      Commit message:


	  
		
 add availableThemes function.
 
    
  
    

      Package: SPICEY

      Commit: 398ae760fa0b45973ca7bee8f22e3a11b10affc1

      Author:  georginafp <georgina.fuentes@upf.edu> 

      Date: 2025-09-08 15:07:38 +0200

      Commit message:


	  
		
 add fnd in description file and fix width figure readme
 
    
  
    

      Package: SPICEY

      Commit: 50b75e39555a5aeab6b5cc562f7994de631d5fad

      Author:  georginafp <georgina.fuentes@upf.edu> 

      Date: 2025-09-08 14:11:58 +0200

      Commit message:


	  
		
 Change R version, add testthat examples, add bioc install, fix typos and code implementation (no repeatitions)
 
    
  
    

      Package: DoReMiTra

      Commit: 0d204c7b4db629a3be8e2490e4654fc458d6a848

      Author:  AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com> 

      Date: 2025-09-08 11:46:20 +0200

      Commit message:


	  
		
 updated news
 
    
  
    

      Package: DoReMiTra

      Commit: dc185d80c4f62ca7f34fb31f611a23c20dbf9b80

      Author:  AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com> 

      Date: 2025-09-08 11:45:49 +0200

      Commit message:


	  
		
 version 0.99.1, bump for rebuilding
 
    
  
    

      Package: DoReMiTra

      Commit: 025692cceb11e9b5be23700971e27c57fea9ea28

      Author:  AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com> 

      Date: 2025-09-08 11:44:37 +0200

      Commit message:


	  
		
 removing .Rproj file from tracked ones
 
    
  
    

      Package: TFEA.ChIP

      Commit: 9e8f094e3351f0f172eedc6e97faf763a6f374ac

      Author:  yosra <yosraberrouayel@gmail.com> 

      Date: 2025-09-08 11:40:34 +0200

      Commit message:


	  
		
 correct bumpv
 
    
  
    

      Package: cellmig

      Commit: 0fb28a2ee63ad9338b62e38e631e13150d0a5313

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-08 10:30:12 +0200

      Commit message:


	  
		
 email corrected and bump
 
    
  
    

      Package: cellmig

      Commit: 2910a0d83eda9355d980d5d5dcf7ccfd72602b09

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-08 09:49:09 +0200

      Commit message:


	  
		
 more tests fixed
 
    
  
    

      Package: cellmig

      Commit: 0eee85d9e6bf348a96a1743dcd00e849a04cb33a

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-08 09:14:54 +0200

      Commit message:


	  
		
 use functional programming to avoid repetitions
 
    
  
    

      Package: cellmig

      Commit: 6d91e3eca39a7597cd8a21410d737b1efb4ad682

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-08 09:14:23 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: GenomicRanges

      Commit: 5f3c5d89ca431ab018870e8b47d61a5851029326

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-07 20:55:35 -0700

      Commit message:


	  
		
 a couple of small tweaks
 
    
  
    

      Package: tidyprint

      Commit: f81219d2b146582d2ad06e9d81a497586908058c

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2025-09-08 12:26:49 +0930

      Commit message:


	  
		
 verison bump
 
    
  
    

      Package: GenomicRanges

      Commit: 577bc992fd932f063c2c00118012984b2ad12895

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-07 16:22:22 -0700

      Commit message:


	  
		
 GenomicRanges 1.61.2: Add makeGPosFromDataFrame()

makeGPosFromDataFrame() is similar to makeGRangesFromDataFrame() but
the data-frame-like input is expected to describe genomic positions
rather than genomic ranges. See '?makeGPosFromDataFrame' for the details
and some examples.
 
    
  
    

      Package: txcutr

      Commit: e01f0e734616ccb191bb176e527e7cd4f23a33b1

      Author:  Mervin M Fansler <mmfansler@gmail.com> 

      Date: 2025-09-07 14:44:28 +0200

      Commit message:


	  
		
 bioc-check lint; refresh readme
 
    
  
    

      Package: txcutr

      Commit: 0fcd627f2cfa4ede8c630026aff6605e5508af1c

      Author:  Mervin M Fansler <mmfansler@gmail.com> 

      Date: 2025-09-07 12:27:47 +0200

      Commit message:


	  
		
 fix suggests; update author; undeprecate
 
    
  
    

      Package: rWikiPathways

      Commit: ab313f2fbfb9f233f43a17a2019089049b348bbf

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2025-09-07 13:23:12 +0200

      Commit message:


	  
		
 Bumped the version and added NEWS
 
    
  
    

      Package: rWikiPathways

      Commit: f912b49c3d9446bdc286f02303487e7ac4a23b50

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2025-09-07 13:17:58 +0200

      Commit message:


	  
		
 Removed an obsolete file
 
    
  
    

      Package: rWikiPathways

      Commit: 66095cf40d0d7069511538a680ef84406457cddf

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2025-09-07 13:16:51 +0200

      Commit message:


	  
		
 Updated the preferred article to cite (Agrawal, 2024 also described the rWikiPathways package)
 
    
  
    

      Package: rWikiPathways

      Commit: cd0ca3920e10aa7849b4b7d437286debc59ca8ea

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2025-09-07 13:01:13 +0200

      Commit message:


	  
		
 Fixed the casing (it redirected, at least now)
 
    
  
    

      Package: rWikiPathways

      Commit: ecc9942a59f1f453d2a33e23c895b62c83b70e82

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2025-09-07 12:59:53 +0200

      Commit message:


	  
		
 Removed an unmaintained package
 
    
  
    

      Package: rWikiPathways

      Commit: fd67a26110895fb22f3bda5144b3ac41bc11fe51

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2025-09-07 12:59:26 +0200

      Commit message:


	  
		
 Better links
 
    
  
    

      Package: rWikiPathways

      Commit: 4822cd9e889bad9c53a0fab408205d2a09061f8b

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2025-09-07 12:40:25 +0200

      Commit message:


	  
		
 Added the latest article
 
    
  
    

      Package: RCX

      Commit: 996b12883b33361afade9ac3e2fae8c12a3697b4

      Author:  Florian J. Auer <florian.auer@informatik.uni-augsburg.de> 

      Date: 2025-09-06 14:48:09 +0200

      Commit message:


	  
		
 fromGraphNEL didn't use the provided arguments for conversion
 
    
  
    

      Package: RCX

      Commit: 227576e976422d3f42edc45a122c0f1c93371da1

      Author:  Florian J. Auer <florian.auer@informatik.uni-augsburg.de> 

      Date: 2025-09-05 18:11:08 +0200

      Commit message:


	  
		
 fromGraphNEL didn't use the provided arguments for conversion
 
    
  
    

      Package: RCX

      Commit: a83dce862f8378860a87a329b472845a08677018

      Author:  Florian J. Auer <florian.auer@informatik.uni-augsburg.de> 

      Date: 2025-09-02 13:09:56 +0200

      Commit message:


	  
		
 fromGraphNEL didn't use the provided arguments for conversion
 
    
  
    

      Package: ClusterGVis

      Commit: 2ff29b77012d474986143245969dc87fd7ec860c

      Author:  JunZhang <64965509+junjunlab@users.noreply.github.com> 

      Date: 2025-09-06 16:50:10 +0800

      Commit message:


	  
		
 revision for bioconductor
 
    
  
    

      Package: spARI

      Commit: 532e4cae63432cbee7044123918f06370d445426

      Author:  Your Name <you@example.com> 

      Date: 2025-09-06 10:23:22 +0800

      Commit message:


	  
		
 0.99.16
 
    
  
    

      Package: limpa

      Commit: a20b32b928d017741409ce1cb3e27c135bb311db

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-09-06 12:17:45 +1000

      Commit message:


	  
		
 limpa 1.1.6
- New function dpcON() to estimate the DPC assuming the oberved-normal model. Should give same output as dpc() but is somewhat faster.
- New function pztbinomSameSizeLogitPBothTails() to compute left and right tail p-values for zero-truncated binomial quantiles.
- readDIANN() now allows user-specified input column names.
- Bug fix to readSpectronaut() when there is only one peptide annotation column.
 
    
  
    

      Package: MSstatsShiny

      Commit: bfd992c289b4b9d068a6fa110f91510c77057ae8

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2025-09-05 16:52:55 -0400

      Commit message:


	  
		
 Bump version to 1.11.5 in DESCRIPTION file 
    
  
    

      Package: MSstatsShiny

      Commit: cb1bcc7d714c74021d23c9bfda7789b395fab876

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2025-09-05 16:03:44 -0400

      Commit message:


	  
		
 feature(diann): Enable support for DIANN 2.0 and parquet files (#114)

 
    
  
    

      Package: MSstatsShiny

      Commit: f5156324bb91fed46772aa21dfb1e7fd55d697dc

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2025-09-05 15:38:20 -0400

      Commit message:


	  
		
 feature(network visualization): Redirect users to INDRA when clicking an edge (#115)

 
    
  
    

      Package: MSstatsBioNet

      Commit: 6330e229cb9190a07f7fd6de43c5da3b1641dbfc

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2025-09-05 15:43:23 -0400

      Commit message:


	  
		
 Bump package version to 1.1.6 
    
  
    

      Package: MSstatsBioNet

      Commit: a293ce098999b1b3bd34d0fb46d94a05db25b49f

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2025-09-05 15:37:48 -0400

      Commit message:


	  
		
 feature(visualizeNetworksWithHTML): Add INDRA link into javascript visualization (#57)

 
    
  
    

      Package: biomaRt

      Commit: 30bff9929fb7cb87b7b6066fc6d98c5e7d88441a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-05 18:53:38 +0200

      Commit message:


	  
		
 Create intermediate variable to simplify conditional
 
    
  
    

      Package: biomaRt

      Commit: 689182877e5f1d98a9afd4cf4c84a10a5bc9af54

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-05 18:52:59 +0200

      Commit message:


	  
		
 Re-render pkg man page
 
    
  
    

      Package: ELViS

      Commit: cf16a41b7fbf12972c14b9fc8caefbfffc095540

      Author:  jlee307@uthsc.edu <jlee307@clr0736.cn.isaac.utk.edu> 

      Date: 2025-09-05 12:38:12 -0400

      Commit message:


	  
		
 Basilisk -> Reticulate
Rsamtools if conda env create fails
 
    
  
    

      Package: igblastr

      Commit: 6f1d231efbcfbc9cd903be3509d7556d4d8e232d

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-05 08:12:03 -0700

      Commit message:


	  
		
 small tweaks
 
    
  
    

      Package: SpectriPy

      Commit: bf2197a9b2132b57013b3261fdfb90be9e7d3e1e

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-09-05 16:26:34 +0200

      Commit message:


	  
		
 Merge pull request #83 from rformassspectrometry/jomain

feat: add various replacement methods 
    
  
    

      Package: SpectriPy

      Commit: f87e01ba3cdef2d5e3aeabbdc9b80c259cb6f7db

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-09-05 15:23:38 +0200

      Commit message:


	  
		
 feat: add various replacement methods

- Add `spectraData<-,MsBackendPy`
- Add `$<-,MsBackendPy`
- Change behaviour of `backendInitialize()` to drop all core spectra variables
  with only missing values before transferring the data to Python.
- Add examples to documentation and the vignette describing which spectra
  variables are transferred and how that can be configured.
 
    
  
    

      Package: stPipe

      Commit: 507e0a0f835b8f6ba1e0b16eed077e4c9890ea6b

      Author:  YangXuuu <xuyang1121wws@gmail.com> 

      Date: 2025-09-05 20:55:10 +1000

      Commit message:


	  
		
 Fix Run_Create_Obj
 
    
  
    

      Package: PMScanR

      Commit: 56f44d6c6c67a52d0d35fb199014fb862ba412f5

      Author:  Damian Czopek <36973370+Dragon96pl@users.noreply.github.com> 

      Date: 2025-09-05 12:33:57 +0200

      Commit message:


	  
		
 Update NEWS.md 
    
  
    

      Package: PMScanR

      Commit: 3e2b8c7b6c339b5f763774b5b55d028651ea312d

      Author:  Damian Czopek <36973370+Dragon96pl@users.noreply.github.com> 

      Date: 2025-09-05 12:30:24 +0200

      Commit message:


	  
		
 Update DESCRIPTION 
    
  
    

      Package: PMScanR

      Commit: 39db349588889208cf403c514ba2aeaff1e42478

      Author:  Dragon96pl <36973370+Dragon96pl@users.noreply.github.com> 

      Date: 2025-09-05 12:29:39 +0200

      Commit message:


	  
		
 Corrected merge on branches
 
    
  
    

      Package: PMScanR

      Commit: cc26411fcf13143f3466a4cd06e7cdb29340b47c

      Author:  Dragon96pl <36973370+Dragon96pl@users.noreply.github.com> 

      Date: 2025-09-05 11:14:43 +0200

      Commit message:


	  
		
 Bioconductor changes
 
    
  
    

      Package: igblastr

      Commit: 612ea9ff9649618e6ca342b7aa45208fcc5bcba7

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-04 22:46:58 -0700

      Commit message:


	  
		
 Rename bcr_browser() to igbrowser(), and deprecate the former.

Also started to work on tabulate_mismatches(), tabulate_insertions(),
and tabulate_deletions().
 
    
  
    

      Package: FinfoMDS

      Commit: 3d1a6fe61690096f26146db28385b30f45057ada

      Author:  soob-kim <sbbkim@ucdavis.edu> 

      Date: 2025-09-05 11:58:39 +0900

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: FinfoMDS

      Commit: 5e20cf0b954de5929e20642d94e5701694c8ef13

      Author:  soob-kim <sbbkim@ucdavis.edu> 

      Date: 2025-09-05 11:54:28 +0900

      Commit message:


	  
		
 Comments from Reviewer @js2264 addressed by S
 
    
  
    

      Package: FinfoMDS

      Commit: 8446b81dd215214eb510ff530ca1760b897cb996

      Author:  Hyu Kim <hskim0000@gmail.com> 

      Date: 2025-09-02 21:32:18 -0400

      Commit message:


	  
		
 Comments from Reviewer @js2264 addressed by H
 
    
  
    

      Package: gVenn

      Commit: 7b8fcedc3d632ce31be093018ca7286953af317a

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2025-09-04 23:55:20 -0400

      Commit message:


	  
		
 increment the patch version number by 1
 
    
  
    

      Package: gVenn

      Commit: b0f29af0e42a11af758794b979b2c288ec1d54d7

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2025-09-04 23:54:10 -0400

      Commit message:


	  
		
 shorter lines and adding more indent
 
    
  
    

      Package: SNPRelate

      Commit: e5bd75357d63357742aae2499777f6c1a4246aa8

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2025-09-04 22:22:06 -0500

      Commit message:


	  
		
 use RhpcBLASctl
 
    
  
    

      Package: tidyprint

      Commit: 72ec0c81f7a5aea2163f98180628d3a0f12ccc56

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2025-09-05 11:49:05 +0930

      Commit message:


	  
		
 resolve biocCheck
 
    
  
    

      Package: tidyprint

      Commit: 44ad32cfa50677e219dc2b645d1a9bfb9e6d443f

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2025-09-05 11:21:32 +0930

      Commit message:


	  
		
 change exported functions
 
    
  
    

      Package: tidyprint

      Commit: dcb4f6e292ff30d10b9d4c291494dabc25288d0a

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2025-09-05 11:03:33 +0930

      Commit message:


	  
		
 change exported functions
 
    
  
    

      Package: tidyprint

      Commit: dde9f1436599d722c0375e1bcf8acbc9fb597cb8

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2025-09-05 10:40:24 +0930

      Commit message:


	  
		
 change exported functions
 
    
  
    

      Package: sfi

      Commit: def0978272f2cfa9f2073176106f302ce32c2b42

      Author:  Miao YU <yufree@live.cn> 

      Date: 2025-09-04 17:55:38 -0400

      Commit message:


	  
		
 Delete sfi.Rproj 
    
  
    

      Package: sfi

      Commit: 77771e5892706d742cf34636f5ba5e4ca920f4c7

      Author:  yufree <yufree@live.cn> 

      Date: 2025-09-04 17:54:11 -0400

      Commit message:


	  
		
 # sfi 0.99.1

* Fix warning for C++ code
* Remove sfi.Rproj from git
 
    
  
    

      Package: cellmig

      Commit: a216d20ecfafd7969165ade3dff93459deaeb9a6

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 23:56:01 +0200

      Commit message:


	  
		
 version bump, man update for package
 
    
  
    

      Package: cellmig

      Commit: 7655e5ef83c2c07bbefd74fde51c7700ba39603b

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 23:06:42 +0200

      Commit message:


	  
		
 remove installation commands, eval=F, in vignettes and bump
 
    
  
    

      Package: cellmig

      Commit: ba735381fb9c99073de72617d7cd2d3948a10242

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 21:54:00 +0200

      Commit message:


	  
		
 first round of review done
 
    
  
    

      Package: biocViews

      Commit: 225a7fc66eff6d537e86063b534e6c4feeef8e6a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-09-04 12:03:30 -0500

      Commit message:


	  
		
 version bump 1.77.4
 
    
  
    

      Package: biocViews

      Commit: 28d31b1dcdb104cb1ca467b458b6a2e09068680d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-09-04 11:43:55 -0500

      Commit message:


	  
		
 update build-dbs.Rd
 
    
  
    

      Package: biocViews

      Commit: b4c39a6349bd3166ac18c208856b736a9394f322

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-09-04 11:36:02 -0500

      Commit message:


	  
		
 fix tools:write_PACKAGES man page name reference
 
    
  
    

      Package: biocViews

      Commit: e22fd2f94573537abd2e8b8352f4c61a5170ee5d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-09-04 11:34:28 -0500

      Commit message:


	  
		
 fix use of middle in DESCRIPTION
 
    
  
    

      Package: biocViews

      Commit: 4298b20c6b8e07a31f17863de662ccbade1fbc12

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-05-24 11:15:17 -0400

      Commit message:


	  
		
 fix NOTE re undefined symbol
 
    
  
    

      Package: biocViews

      Commit: a3d86af1a1d66fa5f0b880aea0ba9b7568935457

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-05-24 11:15:06 -0400

      Commit message:


	  
		
 fix note re: biocViewsVocab
 
    
  
    

      Package: biocViews

      Commit: dfdc1cc7dcb776ef917c4d5fcd0a8f1ea7428fc8

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-05-24 11:14:24 -0400

      Commit message:


	  
		
 update to Authors@R
 
    
  
    

      Package: spatialFDA

      Commit: d89d20e7b98e560af0f9ad97ee78808a5f7a35fe

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-09-04 16:46:09 +0200

      Commit message:


	  
		
 below threshold values are not coloured
 
    
  
    

      Package: spatialFDA

      Commit: ee670f750727213da5288161cfa09f2b570ab6ec

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-09-04 15:36:46 +0200

      Commit message:


	  
		
 new QC, shape in heatmap plot and faster examples with bam
 
    
  
    

      Package: Bioc.gff

      Commit: 30c2f247b04f228acab6cd237d9e1e955248ca86

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-09-04 10:08:49 -0500

      Commit message:


	  
		
 version bump 0.99.13
 
    
  
    

      Package: Bioc.gff

      Commit: 38cdf62a386a5e79c4e8dc1c303803b97c5b21c3

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-09-04 11:02:49 -0400

      Commit message:


	  
		
 remove donttest in examples
 
    
  
    

      Package: Bioc.gff

      Commit: ff9cb1f83238c5f243b30fc7fde38a40c09c2bae

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-09-04 10:44:50 -0400

      Commit message:


	  
		
 version bump 0.99.12
 
    
  
    

      Package: ClustIRR

      Commit: e7d3be7912430d43ba748168fcfaed13325459de

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 15:07:10 +0200

      Commit message:


	  
		
 last bugfix in dco
 
    
  
    

      Package: biocViews

      Commit: 0344561c345bbd27186315d5378912e261c1c16d

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-09-04 08:54:01 -0400

      Commit message:


	  
		
 Closes #20
 
    
  
    

      Package: Ularcirc

      Commit: 990980aed022dfff809198d8c9b129fc8f8076be

      Author:  David Humphreys <dth569@gadi-login-04.gadi.nci.org.au> 

      Date: 2025-09-04 22:09:10 +1000

      Commit message:


	  
		
 Fixing documentation for build
 
    
  
    

      Package: ClustIRR

      Commit: c59d8257d48c7b688ff0259a0b4c46b3801ab1c3

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 14:03:52 +0200

      Commit message:


	  
		
 community split, bump
 
    
  
    

      Package: ClustIRR

      Commit: da4a2ba2bfc87a2263ed12643c42ffbaf9a197b2

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2025-09-04 14:01:38 +0200

      Commit message:


	  
		
 merge
 
    
  
    

      Package: ClustIRR

      Commit: 9347c81bd781065dcc59189edcae467daf401f15

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2025-09-04 13:55:17 +0200

      Commit message:


	  
		
 updated dco.R
 
    
  
    

      Package: ClustIRR

      Commit: c65064efb43e93789e627383903ddc8e3b5db21b

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2025-09-04 13:54:59 +0200

      Commit message:


	  
		
 updated models
 
    
  
    

      Package: ClustIRR

      Commit: 928bf77575d95b69c0f99c9de062189f193f849d

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2025-07-14 16:04:26 +0200

      Commit message:


	  
		
 Merge branch 'main' of github.com:snaketron/ClustIRR
 
    
  
    

      Package: ClustIRR

      Commit: eb433bba0b838418e4240237d3e2742c0b6763bf

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2025-07-14 16:04:17 +0200

      Commit message:


	  
		
 merge
 
    
  
    

      Package: ClustIRR

      Commit: 5db8b954b934e2ae1ce7289fdeffca872e9de922

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 13:47:39 +0200

      Commit message:


	  
		
 man fix
 
    
  
    

      Package: ClustIRR

      Commit: 12c78aeb3705a3009b13c9f07d4dd46b34823b72

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 13:47:22 +0200

      Commit message:


	  
		
 update for 04. Sep. 2025
 
    
  
    

      Package: ClustIRR

      Commit: 3650419a19d14bf23fbde57adab0d29f18ba0848

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 12:53:22 +0200

      Commit message:


	  
		
 bugfix
 
    
  
    

      Package: ClustIRR

      Commit: 9bde1dac769367613d83c3e1b23f340bbb46fb57

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 12:13:57 +0200

      Commit message:


	  
		
 updated NEWS
 
    
  
    

      Package: ClustIRR

      Commit: b33d3f1a9009773d67367e4cd8f84bc2626d0ff2

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 12:13:37 +0200

      Commit message:


	  
		
 fixed T->TRUE, F->FALSE
 
    
  
    

      Package: ClustIRR

      Commit: 6ea6a39eed7010377eeb1dffb6afb30b6223803a

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-09-04 11:51:21 +0200

      Commit message:


	  
		
 update decoding communities, calculating purity
 
    
  
    

      Package: Rarr

      Commit: d4e9538af428173549175634cc1666c1c0e05b7d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 18:09:22 +0200

      Commit message:


	  
		
 Bump version number
 
    
  
    

      Package: Rarr

      Commit: 5f9f401cc05eb6c2c925904b5460fd69bb902a89

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 18:09:03 +0200

      Commit message:


	  
		
 Document renames
 
    
  
    

      Package: Rarr

      Commit: 6e4a03c20572a677918e537ec65ce9a2fb3e3d66

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 17:12:51 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: 28c28eed6105d48c1f9e0641c9ef4dcca6ec387a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 17:12:37 +0200

      Commit message:


	  
		
 Rename path argument to zarr_path

For consistency with read_zmetadata
 
    
  
    

      Package: Rarr

      Commit: 001de5bee74943bd4fedfb81f5a459fffbb8d1a8

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 16:08:59 +0200

      Commit message:


	  
		
 Move missing metadata test file to metadata test folder
 
    
  
    

      Package: Rarr

      Commit: 3e20809f72da582da1e382381f07c8ef49ffcee0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 16:07:01 +0200

      Commit message:


	  
		
 Use leading dot in name for internal functions
 
    
  
    

      Package: Rarr

      Commit: 862d7058d4163f103b1f01c9e82b83c886f66ac6

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 16:05:48 +0200

      Commit message:


	  
		
 Add venv to Rbuildignore
 
    
  
    

      Package: Rarr

      Commit: 5d38a040db5948445acced5385b3ff8711a0930c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 14:54:53 +0200

      Commit message:


	  
		
 Add test for read_zmetadata
 
    
  
    

      Package: Rarr

      Commit: 8af73ba5d37a2a5aaccd065332a6db3778038d68

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 14:16:20 +0200

      Commit message:


	  
		
 Explain what .zmetadata is in roxygen block
 
    
  
    

      Package: Rarr

      Commit: aa8a846d6df820936257e899d7d24f79b77b67a6

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 14:15:16 +0200

      Commit message:


	  
		
 Restore sys-lib testing mechanism

To test both system and bundled version of Blosc & Rarr
 
    
  
    

      Package: Rsubread

      Commit: 5bf87c530c3b85a2599de98f5e81d647b076d7cb

      Author:  Yang Liao (Monash University) <yliao@m3v109.massive.org.au> 

      Date: 2025-09-04 12:29:06 +1000

      Commit message:


	  
		
 Added junction.counts in output of cellCounts
 
    
  
    

      Package: ChIPanalyser

      Commit: 27504b973bb0c939ea58f0b46b410305839b057d

      Author:  patrickCNMartin <pcnmartin@gmail.com> 

      Date: 2025-09-03 11:37:38 -0700

      Commit message:


	  
		
 readme update
 
    
  
    

      Package: ChIPanalyser

      Commit: 2802681ca65943b679dedd6548e46b160e221893

      Author:  patrickCNMartin <pcnmartin@gmail.com> 

      Date: 2025-09-03 11:26:43 -0700

      Commit message:


	  
		
 plot occupancy update
 
    
  
    

      Package: spARI

      Commit: da771726f9800143a2f828881006e0c98ff0aa74

      Author:  Your Name <you@example.com> 

      Date: 2025-09-04 02:15:31 +0800

      Commit message:


	  
		
 0.99.15
 
    
  
    

      Package: spARI

      Commit: cdc3976d105403040a1d26e3a99909d1d80dc14f

      Author:  Your Name <you@example.com> 

      Date: 2025-09-04 02:12:18 +0800

      Commit message:


	  
		
 0.99.14
 
    
  
    

      Package: spARI

      Commit: 2cef2f69575f607b3262f27e5644a63bb66c45dd

      Author:  Your Name <you@example.com> 

      Date: 2025-09-04 01:57:21 +0800

      Commit message:


	  
		
 0.99.13
 
    
  
    

      Package: scToppR

      Commit: c792a1db872fd78947c02f43bb4705174a0c16bf

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-09-03 12:35:59 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: scToppR

      Commit: f845e26dc22aed09fd0322c2da59315bc312f2d4

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-09-03 12:23:01 -0400

      Commit message:


	  
		
 vignette package load
 
    
  
    

      Package: scToppR

      Commit: 5207bed0d4a95fd3bceaa085e4a7b0f80717449b

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-09-03 12:17:32 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: scToppR

      Commit: 08a723da5ad5981ffb8dc1a1d11def17ea29a7bb

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-09-03 12:16:49 -0400

      Commit message:


	  
		
 update man files
 
    
  
    

      Package: BgeeDB

      Commit: 6b7e351d3c06e63b2086abbab6c72b92a88ccf66

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2025-09-03 17:46:46 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: BgeeDB

      Commit: a73056a9cb5b3b5437612b145e897b5adeacd242

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2025-09-03 17:44:04 +0200

      Commit message:


	  
		
 correct descendant retrieval for cellTypes and updated overal code quality
 
    
  
    

      Package: scToppR

      Commit: f0c53cc3a2e938403af7696e15021214f7143726

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-09-03 11:40:56 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: scToppR

      Commit: a69f439fbefb925d2e7be899fe7c31f99ab1f48d

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-09-03 11:29:09 -0400

      Commit message:


	  
		
 cluster_col bug
 
    
  
    

      Package: scToppR

      Commit: 1b32c8e0d8c618d7b2aacef0e5c6e368eb4ff679

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-08-27 12:30:55 -0400

      Commit message:


	  
		
 vignette fix
 
    
  
    

      Package: scToppR

      Commit: 6da9a1ac0d762f73fa0c64adccc55f953bbb16ac

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-08-27 11:30:31 -0400

      Commit message:


	  
		
 httr2 update
 
    
  
    

      Package: scToppR

      Commit: 435a5c4042029a3f101cac0a893fd7ebbd4e22e8

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-05-01 10:41:36 -0400

      Commit message:


	  
		
 plot tweak
 
    
  
    

      Package: scToppR

      Commit: f24a991fbc526fc7dbb0bed68c93bd0f90eb2147

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-05-01 10:33:41 -0400

      Commit message:


	  
		
 add httr2
 
    
  
    

      Package: scToppR

      Commit: ff2135bdcd0385eaeb8832a00a1156535e13099b

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-04-01 13:39:18 -0400

      Commit message:


	  
		
 toppplot has 3 p's
 
    
  
    

      Package: scToppR

      Commit: 1e2f8635d0f5749bd14d611af940fa26d9699444

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-04-01 13:38:10 -0400

      Commit message:


	  
		
 readme update
 
    
  
    

      Package: scToppR

      Commit: cdee66f5813a2c95dd9cdfb8b730129d85cbd478

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-04-01 13:37:38 -0400

      Commit message:


	  
		
 readme update
 
    
  
    

      Package: scToppR

      Commit: e77e9abf6534b4a24eed78b6ed0d7f70fcde9492

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-04-01 13:36:24 -0400

      Commit message:


	  
		
 example updates
 
    
  
    

      Package: scToppR

      Commit: 2d3b885ebdabe470184ed605150b5a0e0623c148

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-04-01 13:21:26 -0400

      Commit message:


	  
		
 new data and marker list inputs
 
    
  
    

      Package: scToppR

      Commit: f7451da58e9b1e1ffa99cbf80d0aab0411d972de

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2025-03-25 12:25:33 -0400

      Commit message:


	  
		
 marker update
 
    
  
    

      Package: GEOquery

      Commit: 414557bd7d999b5c54c5c74478a834910929ac00

      Author:  Sean Davis <seandavi@gmail.com> 

      Date: 2025-09-03 10:54:23 -0400

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: GEOquery

      Commit: 77e01add4f7ecc751258ed8bada9a6ba894ada38

      Author:  Sean Davis <seandavi@gmail.com> 

      Date: 2025-09-03 10:53:49 -0400

      Commit message:


	  
		
 Add skeleton single-cell vignette
 
    
  
    

      Package: GOexpress

      Commit: 1f9c4631c489a3594004b147715ff1796bf333b2

      Author:  Kevin Rue <kevinrue@users.noreply.github.com> 

      Date: 2025-09-03 14:40:13 +0100

      Commit message:


	  
		
 update version and contributors
 
    
  
    

      Package: GOexpress

      Commit: 3eb4d2c3d79dd067888b33596a228ed67cc185f2

      Author:  Kevin Rue <kevinrue@users.noreply.github.com> 

      Date: 2025-09-03 14:38:06 +0100

      Commit message:


	  
		
 remove all mentions of curl
 
    
  
    

      Package: GOexpress

      Commit: a87dbb995d8b28e9502e83748d99faa2630f6c8c

      Author:  Kevin Rue <kevinrue@users.noreply.github.com> 

      Date: 2025-09-03 14:36:58 +0100

      Commit message:


	  
		
 Merge branch 'master' of github.com:kevinrue/GOexpress
 
    
  
    

      Package: GOexpress

      Commit: b6de86f80d8fbd89717dbb4ee02cc6f019ca33b0

      Author:  Kevin Rue-Albrecht <kevinrue67@gmail.com> 

      Date: 2025-09-03 14:36:28 +0100

      Commit message:


	  
		
 Merge pull request #4 from Bisaloo/fix-biomaRt-warnings

Remove deprecated curl argument in biomaRt::getBM() 
    
  
    

      Package: GOexpress

      Commit: 532783a3a569f088315008293367ab55788c62e4

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 08:37:34 +0200

      Commit message:


	  
		
 Remove deprecated curl argument in biomaRt::getBM()

Fix R CMD check WARNING
 
    
  
    

      Package: peakCombiner

      Commit: fd2507d12524248b9cb36c16fe72d0e531332013

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-09-03 15:34:08 +0200

      Commit message:


	  
		
 Update DESCRIPTION 
    
  
    

      Package: peakCombiner

      Commit: 91c71442590a153dcea373f1583ff85dc9e6756d

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-09-03 15:18:05 +0200

      Commit message:


	  
		
 Delete tests/.DS_Store 
    
  
    

      Package: peakCombiner

      Commit: ac521e8a077b0d5d0cb8baf2abd39755fbb5a9f7

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-09-03 15:16:35 +0200

      Commit message:


	  
		
 Update .gitignore 
    
  
    

      Package: peakCombiner

      Commit: 66017b08fbcebd279e174f3f5deb2c34ee773d23

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-09-03 15:15:38 +0200

      Commit message:


	  
		
 Update .gitignore 
    
  
    

      Package: mzR

      Commit: 15fde15ae6ef3e59130acd5779e2fcd04f537eea

      Author:  Adriano Rutz <44283913+Adafede@users.noreply.github.com> 

      Date: 2025-09-02 15:59:24 +0200

      Commit message:


	  
		
 Merge pull request #1 from jorainer/adafede

Make electronBeamEnergy an optional header column for export 
    
  
    

      Package: mzR

      Commit: 57c02f0d62d4935df07753e097909fc3c892d65e

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-09-02 15:37:37 +0200

      Commit message:


	  
		
 fix unit test
 
    
  
    

      Package: mzR

      Commit: ff6dbf10b12786f35b22506ffeec31d998f42836

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-09-02 15:29:42 +0200

      Commit message:


	  
		
 refactor: make electronBeamEnergy an optional header column
 
    
  
    

      Package: mzR

      Commit: 3c9edb060cda9185564fcf3a14ef3ac45719b6b3

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-09-02 10:13:59 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'adafede/devel' into adafede
 
    
  
    

      Package: mzR

      Commit: b45041090cc617e41507359491ba5cb74c0d62e8

      Author:  Adriano Rutz <44283913+Adafede@users.noreply.github.com> 

      Date: 2025-08-20 14:34:21 +0200

      Commit message:


	  
		
 Update DESCRIPTION

https://github.com/sneumann/mzR/pull/311#issuecomment-3205487869 
    
  
    

      Package: peakCombiner

      Commit: c19cd07c030c024fb7c9b05f1e2049e69e05fb44

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-09-03 13:59:57 +0200

      Commit message:


	  
		
 Update DESCRIPTION version 
    
  
    

      Package: peakCombiner

      Commit: e9102c2d3e230132f620d71b229f725f08fb1aca

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-09-03 13:55:35 +0200

      Commit message:


	  
		
 Delete peakCombiner.Rproj 
    
  
    

      Package: islify

      Commit: c295fbfac0e992f6abc7edc94adb027671e05b3a

      Author:  Jakob Theorell <jakob.theorell@ki.se> 

      Date: 2025-09-03 12:44:26 +0200

      Commit message:


	  
		
 The "problematicUnevenDistribution" flag is introduced.
 
    
  
    

      Package: msa

      Commit: 946360ddd9ad51ae44141723b19898750f8186be

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2025-09-03 12:22:33 +0200

      Commit message:


	  
		
 pull request from Rong-Zh merged to fix memory leak in Muscle; version number bumped to 1.41.2
 
    
  
    

      Package: msa

      Commit: 8f150f08f5011d5b040f6eabe583d765e1fa1a79

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2025-09-03 12:19:34 +0200

      Commit message:


	  
		
 Merge pull request #38 from Rong-Zh/devel

Fix memory leak 
    
  
    

      Package: msa

      Commit: 464c95ba38420af174a778ba88c478cb0a4c4c50

      Author:  Rong-Zh <zerelove@icloud.com> 

      Date: 2025-05-12 11:06:58 +0800

      Commit message:


	  
		
 Fix memory leak
 
    
  
    

      Package: DMRcaller

      Commit: 840d78ca2e287e0b51ffbceb675633cb7dd4078e

      Author:  nrzabet <r.zabet@qmul.ac.uk> 

      Date: 2025-09-03 11:28:17 +0100

      Commit message:


	  
		
 added support for ONT methylation data
 
    
  
    

      Package: DMRcaller

      Commit: fa43084717c15ec0d3b5498dd9622d9f8b6930a7

      Author:  nrzabet <r.zabet@qmul.ac.uk> 

      Date: 2025-09-03 11:27:31 +0100

      Commit message:


	  
		
 added support for ONT methylation data
 
    
  
    

      Package: SingleCellAlleleExperiment

      Commit: 51fab37dd964d172d51e3d2223befd43097215a0

      Author:  jonas-schuck <jonas_schuck@hotmail.de> 

      Date: 2025-09-03 11:37:02 +0200

      Commit message:


	  
		
 Adressing devel error for failing test after DropletUtils package update; Minor documentation update; version bump v1.5.1
 
    
  
    

      Package: SingleCellAlleleExperiment

      Commit: 641fa2f8b5d3082a6d99a450203856fe784f365c

      Author:  jonas-schuck <jonas_schuck@hotmail.de> 

      Date: 2025-09-03 09:51:59 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel' into devel
Merging upstream/devel into origin/devel to work on 3.22/devel test-errors
 
    
  
    

      Package: SingleCellAlleleExperiment

      Commit: 98eb7bfe150daea5c8efd43b32897982d592fda7

      Author:  Jonas Schuck <106832949+Jonas-Schuck@users.noreply.github.com> 

      Date: 2025-08-27 13:19:54 +0200

      Commit message:


	  
		
 Merge pull request #10 from AGImkeller/fixing_GHA

updating GHA to a more recent cache version 
    
  
    

      Package: SingleCellAlleleExperiment

      Commit: 016d0e1f3f976d2e69cd312b27a29633a2036749

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2025-03-18 17:00:19 +0100

      Commit message:


	  
		
 while at it: updating the version of roxygen being used
 
    
  
    

      Package: SingleCellAlleleExperiment

      Commit: 55530191c5c1870096e3b2f600e3c115d13e9ad3

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2025-03-07 14:39:14 +0100

      Commit message:


	  
		
 updating GHA to a more recent cache version
 
    
  
    

      Package: biomaRt

      Commit: 8b8b9731a557581cc3ffe9f969596be990f6bbb9

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-03 11:19:05 +0200

      Commit message:


	  
		
 Fix partial matching warnings
 
    
  
    

      Package: ChIPDBData

      Commit: 929bc6bcc5b6e2fe4512c80f4a793028a398485a

      Author:  yosra <yosraberrouayel@gmail.com> 

      Date: 2025-09-03 10:56:21 +0200

      Commit message:


	  
		
 review changes
 
    
  
    

      Package: spatialFDA

      Commit: 2b4a687a48309bc4a8d0697dcc8c5585060fc180

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-09-02 15:26:55 +0200

      Commit message:


	  
		
 new test and better code for RSE calc
 
    
  
    

      Package: spatialFDA

      Commit: 768c4ec4e41a41c475ad52fbf0778b9ad7bdd55d

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-09-01 18:45:03 +0200

      Commit message:


	  
		
 implemented RSE TODO: write some assertions and tests
 
    
  
    

      Package: spatialFDA

      Commit: bbc5e97a9c228786bca8dd6ddab16f048bfbe7be

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-09-01 11:09:27 +0200

      Commit message:


	  
		
 changed to residual sum of squares per condition
 
    
  
    

      Package: Spectra

      Commit: 9e851b5421a81d718c1a642f12e60f8c695d9275

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-09-03 08:56:02 +0200

      Commit message:


	  
		
 Merge pull request #365 from rformassspectrometry/jomain

Add default implementation for replacement methods 
    
  
    

      Package: Spectra

      Commit: 865f8574d0c65687ac155f09103616a7f315641e

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-09-03 08:24:37 +0200

      Commit message:


	  
		
 refactor: define additional defaults for replacement methods
 
    
  
    

      Package: Spectra

      Commit: ee963717aa4d86fa1b5740ac7ee7aacba35bfcaa

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-09-02 09:57:23 +0200

      Commit message:


	  
		
 format: reformat applyProcessing code
 
    
  
    

      Package: Rsubread

      Commit: d014fc48731e3b2859598aae1f7338817660c438

      Author:  Yang Liao (Monash University) <yliao@m3v109.massive.org.au> 

      Date: 2025-09-03 11:30:57 +1000

      Commit message:


	  
		
 Multiple-sample cellCounts junction detection.
 
    
  
    

      Package: Rsamtools

      Commit: 47580dee3954e206d8b8b348b8c26553ff014678

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-02 17:47:55 -0700

      Commit message:


	  
		
 Rsamtools 2.25.3: Fix compillation problem on FreeBSD

See https://github.com/Bioconductor/Rsamtools/issues/66

Also add VariantAnnotation to Suggests.
 
    
  
    

      Package: GEOquery

      Commit: 92adad8c3737494237a3aba091334c9b62335d28

      Author:  Sean Davis <seandavi@gmail.com> 

      Date: 2025-09-02 20:31:08 -0400

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: GEOquery

      Commit: 558d8c28553e020d5ad89a95073dc12c16d4e4e2

      Author:  Sean Davis <seandavi@gmail.com> 

      Date: 2025-09-02 20:30:33 -0400

      Commit message:


	  
		
 Add capability to read GSE file listing

The GEO series records often include .tar files.
This added functionality exposes the contents of
a hidden (not accessible from the website) file
listing the contents of the files and .tar archive.
 
    
  
    

      Package: gemma.R

      Commit: eededbe4847d332fdcf9e1cb77988175d880d3bc

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2025-09-02 15:52:30 -0700

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: gemma.R

      Commit: 206bf1f762b0aca37a87b496708b490950acccf4

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2025-09-02 15:52:14 -0700

      Commit message:


	  
		
 fix vignette for changed annotations
 
    
  
    

      Package: SeqArray

      Commit: 24e176dac79eaa01e5d4bfe714562a72d6b0dad5

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2025-09-02 17:50:41 -0500

      Commit message:


	  
		
 fix
 
    
  
    

      Package: smoothclust

      Commit: 28375eec19cc43dda89fa2ea3e2312fbbabb39b1

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-09-02 17:33:54 -0400

      Commit message:


	  
		
 version bump for testing
 
    
  
    

      Package: GEOquery

      Commit: 461800696a967c11d8cb691b8e601d4f58a352b3

      Author:  Sean Davis <seandavi@gmail.com> 

      Date: 2025-09-02 17:11:49 -0400

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: GEOquery

      Commit: 134a0ce06f64ae0b1026c91e9a1019d2a8a5ed53

      Author:  Sean Davis <seandavi@gmail.com> 

      Date: 2025-09-02 17:11:10 -0400

      Commit message:


	  
		
 refactor supplemental file handling

* Split out some functionality to separate functions
* Partial conversion to use 
 </pre>
    </div>
  
    

      Package: MetaboDynamics

      Commit: 2280d3fae90b9482b88006d91a1dcd1edbd36cee

      Author:  Katja Danielzik <katja.danielzik@stud.uni-due.de> 

      Date: 2025-09-02 20:43:13 +0200

      Commit message:


	  
		
 internal: euclidean distance and cell count model, longitudinalMetabolimics with simulated cell counts
 
    
  
    

      Package: assorthead

      Commit: a4768f36a734f43db3eae4841ce4496e78fc22e8

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-09-02 11:08:21 -0700

      Commit message:


	  
		
 Updated the vendored aarand, sanisizer and kmeans libraries.
 
    
  
    

      Package: MethylSeekR

      Commit: 8c943ee3abbc306ab6feff5e97ff78c9f6c13c6e

      Author:  LukasBurger <lukas.burger@fmi.ch> 

      Date: 2025-09-02 16:00:32 +0200

      Commit message:


	  
		
 bumped up version number
 
    
  
    

      Package: MethylSeekR

      Commit: 954ace29f926fe3be4395f9a0b877619578384bf

      Author:  LukasBurger <lukas.burger@fmi.ch> 

      Date: 2025-09-02 15:57:57 +0200

      Commit message:


	  
		
 Merge branch 'devel' of git.bioconductor.org:packages/MethylSeekR into devel
 
    
  
    

      Package: MethylSeekR

      Commit: cea09d1bd51345eff6b5e5937e22ea329f81da65

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-26 15:27:17 +0200

      Commit message:


	  
		
 fixed dependency
 
    
  
    

      Package: MethylSeekR

      Commit: a90891d344b14eccd365e3d91ce7db445f5f30ed

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-19 13:55:10 +0200

      Commit message:


	  
		
 -add imports
 
    
  
    

      Package: MethylSeekR

      Commit: ae16de2894a149340627abe09c1aa4e30218e853

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-12 09:23:17 +0200

      Commit message:


	  
		
 bumped up the version number
 
    
  
    

      Package: MethylSeekR

      Commit: e3b0562d571973d1ccb7c59c9b7c541edf630ee1

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-05 09:42:11 +0200

      Commit message:


	  
		
 added GenomeInfoDb to Suggests in DESCRIPTION file
 
    
  
    

      Package: MethylSeekR

      Commit: efb31e260fd2be0a2e1310c552e07d91a048c4a4

      Author:  Michael Stadler <stadler.michael@gmail.com> 

      Date: 2021-06-21 08:13:09 +0200

      Commit message:


	  
		
 try without discontinued gfortran cask on macOS 
    
  
    

      Package: MethylSeekR

      Commit: d53baab8ec5bc16348fe416874d5edc89bd2104a

      Author:  Michael Stadler <stadler.michael@gmail.com> 

      Date: 2021-06-07 12:25:32 +0200

      Commit message:


	  
		
 use release R (4.1) for BioC devel (3.14) 
    
  
    

      Package: HiCaptuRe

      Commit: f42ac200e4d5862bc8c5e2b111423bcb0147c80f

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2025-09-02 14:42:21 +0200

      Commit message:


	  
		
 update docs, minor note and version bump
 
    
  
    

      Package: scRNAseqApp

      Commit: a9306a164c4055ad63419fa81fe5d138ea6b144a

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-09-02 08:21:16 -0400

      Commit message:


	  
		
 add flex-wrap for newcomment-form.
 
    
  
    

      Package: MetaboDynamics

      Commit: 4931ccf3ac7590e287b04302de51e041317496b7

      Author:  Katja Danielzik <katja.danielzik@stud.uni-due.de> 

      Date: 2025-09-02 14:10:18 +0200

      Commit message:


	  
		
 delta_t now as list of ordered visualizations
 
    
  
    

      Package: HiCaptuRe

      Commit: eaa3eadeac195cb69b5dad2080f07787135615c0

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2025-09-02 14:02:04 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: biomaRt

      Commit: 00d5f87f57d6da035b43920c63f753f6457ed48a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:29:36 +0200

      Commit message:


	  
		
 Add extra step to convert NEWS to md in pkgdown workflow
 
    
  
    

      Package: biomaRt

      Commit: 291e571e627177692ad31091edb4d6c1772ccfa5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:21:18 +0200

      Commit message:


	  
		
 Document creation  of pkgdown website
 
    
  
    

      Package: biomaRt

      Commit: d47915291a6be4011d03769e93bb8cf93db6815c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:10:12 +0200

      Commit message:


	  
		
 Add Hugo as ctb
 
    
  
    

      Package: biomaRt

      Commit: 2abc4be3a69a7091f8a53c3dee77f92ac38b004a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:09:28 +0200

      Commit message:


	  
		
 Add de.NBI as funder
 
    
  
    

      Package: biomaRt

      Commit: 19e207439f9d5be24eecf39401386c7bd270ea51

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 21:46:02 +0200

      Commit message:


	  
		
 Add logo
 
    
  
    

      Package: biomaRt

      Commit: 399fc490a20a02dd42da849c188f5fd1d4131d5f

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 17:05:33 +0200

      Commit message:


	  
		
 Create pkgdown reference index
 
    
  
    

      Package: biomaRt

      Commit: fc90cc2b3485c84fc63db82ac63948f1c7e44819

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 16:36:52 +0200

      Commit message:


	  
		
 Customize pkgdown GitHub Action for bioC
 
    
  
    

      Package: biomaRt

      Commit: 7b306f7aa916268b52c8ffc692037bde8079eec4

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 16:33:45 +0200

      Commit message:


	  
		
 Get pkgdown github action from r-lib
 
    
  
    

      Package: biomaRt

      Commit: 0c423bec9b00d7bc3e0fec5f8904659237bc9cb2

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:01:12 +0200

      Commit message:


	  
		
 Set up pkgdown
 
    
  
    

      Package: HiCaptuRe

      Commit: 52ce5ba1650f891db8cb8a31059b9caae0ec7def

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2025-09-02 13:17:14 +0200

      Commit message:


	  
		
 change invert default to FALSE
 
    
  
    

      Package: igblastr

      Commit: f61b1d0d8f87292a26d3f23556877bee798a7266

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-02 00:16:11 -0700

      Commit message:


	  
		
 small tweak to README.md
 
    
  
    

      Package: igblastr

      Commit: a3015435d053cb9700a149da7da4eff0fc137a68

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-01 23:22:08 -0700

      Commit message:


	  
		
 igblastr 0.99.15

Update list of built-in C-region dbs from:

  db_name                         C
  _IMGT.human.IGH+IGK+IGL.202412 76
  _IMGT.mouse.IGH.202412         31
  _IMGT.rabbit.IGH.202412        28
  _IMGT.rat.IGH.202508           18

to:

  db_name                                 C
  _IMGT.human.IGH+IGK+IGL.202412         76
  _IMGT.mouse.IGH.202509                 56
  _IMGT.rabbit.IGH.202412                28
  _IMGT.rat.IGH.202508                   18
  _IMGT.rhesus_monkey.IGH+IGK+IGL.202509 40

Note the updated db for mouse and the new db for rhesus monkey.

This new list reflects what's listed in the bottom left table at
https://www.imgt.org/vquest/refseqh.html on Sep 1, 2025 (ignoring Alpaca).
 
    
  
    

      Package: variancePartition

      Commit: e421210f3406bd07fdaf4c31d6bb572886189664

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2025-09-01 21:20:59 -0400

      Commit message:


	  
		
 1.39.2
 
    
  
    

      Package: EpipwR

      Commit: 191281918ca6722fb49c70528cf931d583fb0ee1

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-09-01 11:49:04 -0500

      Commit message:


	  
		
 Merge to main
 
    
  
    

      Package: EpipwR

      Commit: 1eb710367a96f268b812f79eeecbee6675174e64

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-09-01 11:48:55 -0500

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: EpipwR

      Commit: 80e6fabeb89138e1baea7cf612eb8d543691432d

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-09-01 11:33:02 -0500

      Commit message:


	  
		
 Minor updates
 
    
  
    

      Package: EpipwR

      Commit: 8f9943816475b340231d24bc52bb5707edb18cfb

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-08-04 14:55:19 -0500

      Commit message:


	  
		
 Updated README
 
    
  
    

      Package: EpipwR

      Commit: c1bf9b72b37d63256702926c5a3d7c04b34a2e74

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-08-04 14:48:15 -0500

      Commit message:


	  
		
 New pwrE_to_EpipwR function
 
    
  
    

      Package: EpipwR

      Commit: cc492478e8c15ef79791eea2e1154880a4296dab

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-04-16 10:01:51 -0500

      Commit message:


	  
		
 Update for custom phenotype data
 
    
  
    

      Package: EpipwR

      Commit: bbb9a9d6fa5b84e89c254ea6f8221dcda1ee7a63

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2024-12-04 09:37:06 -0600

      Commit message:


	  
		
 Remove .Rhistory
 
    
  
    

      Package: EpipwR

      Commit: 78633367f47c11b0b4ddc766d67d12e9d49c89ea

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2024-12-04 09:32:05 -0600

      Commit message:


	  
		
 Added "Custom" option for Tissue parameter
 
    
  
    

      Package: smoppix

      Commit: b943a7e69eed644547e1a416bf1df3d817b224f2

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-09-01 15:16:31 +0200

      Commit message:


	  
		
 Installer from biconductor
 
    
  
    

      Package: smoppix

      Commit: 85959e42dc13a7714d901d47eb0bd2cc420977d9

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-09-01 10:32:10 +0200

      Commit message:


	  
		
 Simplify readme header
 
    
  
    

      Package: smoppix

      Commit: 35518358ab29c988cd8ce2e2ecabbf0f98461f65

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-29 16:08:18 +0200

      Commit message:


	  
		
 Remove superfluous test
 
    
  
    

      Package: smoppix

      Commit: f071e79c4517453e7cf5f99b4b4092fe5073bfee

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 17:17:38 +0200

      Commit message:


	  
		
 Without colons
 
    
  
    

      Package: smoppix

      Commit: 267ee1476db8cee2a9cdbe017d3d904b52bd9cad

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 17:08:52 +0200

      Commit message:


	  
		
 also document namespace bplapply change
 
    
  
    

      Package: smoppix

      Commit: 575847312d4d38d64a5d264186bde1853ae48da0

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 17:08:34 +0200

      Commit message:


	  
		
 Avoid namespace headaches
 
    
  
    

      Package: smoppix

      Commit: 68daccae6cf2f5d77f6084cc146bae70df989571

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 15:36:17 +0200

      Commit message:


	  
		
 keep namesin loadbalancelappy
 
    
  
    

      Package: smoppix

      Commit: c68711d8d2d833cba216c7be67e79e24d2c42760

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 15:21:29 +0200

      Commit message:


	  
		
 no longer store result for loadbalancebplapply
 
    
  
    

      Package: edgeR

      Commit: 1fe6a4d26b82466ae10194759b59ce372c3d332a

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-09-01 20:47:38 +1000

      Commit message:


	  
		
 edgeR 4.7.4
- chooseLowessSpan() now used to choose span for voomLmFit(), estimateDisp() and WLEB().
- Revise help page for diffSplice.DGEGLM().
 
    
  
    

      Package: Rarr

      Commit: ad154ea58f37669bcb515d8961c77625d2c6e874

      Author:  Sharla Gelfand <sharla.gelfand@gmail.com> 

      Date: 2025-08-29 12:07:53 -0400

      Commit message:


	  
		
 Error when no metadata found (#37)


 
    
  
    

      Package: biomaRt

      Commit: 933c3bc84d833394b97da9a9cd94bcba382a3fba

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 20:20:14 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: biomaRt

      Commit: 6a7d8977c2ccf9f092ad494387531141eacf95a2

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:51:48 +0200

      Commit message:


	  
		
 Avoid creating new duplicated var
 
    
  
    

      Package: biomaRt

      Commit: e7e78c4b84f44f2731db95ededd9c62b217bff91

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:44:37 +0200

      Commit message:


	  
		
 Specify default for pattern in function arguments
 
    
  
    

      Package: biomaRt

      Commit: 480255502a516a96143d8c401cfc612349fb818b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:41:06 +0200

      Commit message:


	  
		
 Remove superseded code chunk

Since a scheme is always added at the beginning of this function
 
    
  
    

      Package: biomaRt

      Commit: 49e9bac8f1fc048c77ba72dfcbe93c911737f477

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:40:20 +0200

      Commit message:


	  
		
 Use nzchar()
 
    
  
    

      Package: biomaRt

      Commit: 796ffcb7d29a79f814bcc01f6fe18c5dd3176fc9

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:40:09 +0200

      Commit message:


	  
		
 Simplify pastes
 
    
  
    

      Package: biomaRt

      Commit: 3fa9b171c967de42754cdca65f46196dc0bffaa1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:39:40 +0200

      Commit message:


	  
		
 Close connection on.exit()
 
    
  
    

      Package: biomaRt

      Commit: 3a0da35f2d8ecea8e82d8fa0c3ceed06581f3e92

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:39:01 +0200

      Commit message:


	  
		
 Fix typos
 
    
  
    

      Package: Pirat

      Commit: ea23c431ea9f9df6244ffc3e63db0bbee1c5b953

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-09-01 00:10:04 -0700

      Commit message:


	  
		
 Add coma
 
    
  
    

      Package: Pirat

      Commit: 8029b7fb365bdb1d00dd677991802f8d3044692e

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-09-01 00:08:16 -0700

      Commit message:


	  
		
 Add coma
 
    
  
    

      Package: spARI

      Commit: de1f7eb76b545121bcf5cb1125ea6f0e0d27de97

      Author:  Your Name <you@example.com> 

      Date: 2025-09-01 12:07:55 +0800

      Commit message:


	  
		
 commit 0.99.12
 
    
  
    

      Package: DMRcate

      Commit: 607fe30e7b9e1b9d7e18dc173fc18f3eec9b1785

      Author:  timpet <t.peters@garvan.org.au> 

      Date: 2025-08-31 17:13:55 +1000

      Commit message:


	  
		
 DMRcate_3.5.2
 
    
  
    

      Package: ProteinGymR

      Commit: 047692d35ebd532bd547074be1f9a130de44ef84

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 18:01:05 -0400

      Commit message:


	  
		
 bump DEVEL version
 
    
  
    

      Package: ProteinGymR

      Commit: 9808d005d0283030b80502f1882821c5486754fa

      Author:  Tram Nguyen <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 17:55:32 -0400

      Commit message:


	  
		
 Merge branch 'RELEASE_3_21' into devel 
    
  
    

      Package: ProteinGymR

      Commit: bbd7f05257ea9e58a7794c54554d19442431b33e

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-07-17 13:57:35 +0000

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: ProteinGymR

      Commit: aa42a376c9efe9b78dd168b15168812fc3a367c1

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-07-17 13:56:31 +0000

      Commit message:


	  
		
 finished merging
 
    
  
    

      Package: ProteinGymR

      Commit: 73273a5e12c285cd22b886d226cd2537d2b63387

      Author:  Tram Nguyen <tram_nguyen@hms.harvard.edu> 

      Date: 2025-07-17 09:39:26 -0400

      Commit message:


	  
		
 Merge pull request #49 from ccb-hms/devel

merge additional edits from devel 
    
  
    

      Package: ProteinGymR

      Commit: 29b29d0c5702c6fcf3ff64bf7bb25c30bd5471b3

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:42:40 +0000

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: ProteinGymR

      Commit: 760b73857858c6cef78180808d7202ca4e95040d

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:41:33 +0000

      Commit message:


	  
		
 move plotting dependencies to Suggests
 
    
  
    

      Package: ProteinGymR

      Commit: 13bd9181371fcbd4c7ae57be8cf86fecb8b238fb

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:19:17 +0000

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: ProteinGymR

      Commit: 5c2e807546973c6e1944d22a0f4cf7417a02f986

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:18:55 +0000

      Commit message:


	  
		
 reduce `plot_dms_heatmap` dependencies
 
    
  
    

      Package: spARI

      Commit: 8d85e533e33d3e0ad6003560a0f8920af49184ef

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 23:33:20 +0800

      Commit message:


	  
		
 commit 0.99.11
 
    
  
    

      Package: spARI

      Commit: 345b5cc382e55fca417fd2d2ddc2fb9e37788228

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 23:19:37 +0800

      Commit message:


	  
		
 commit 0.99.10
 
    
  
    

      Package: spARI

      Commit: 0280f4d45a493a1866192f3471e9570fea57e23a

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 23:04:52 +0800

      Commit message:


	  
		
 commit 0.99.9
 
    
  
    

      Package: spARI

      Commit: 24d527e7ee838a36b50c1ba9baad7ce0cb75ad76

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 22:21:13 +0800

      Commit message:


	  
		
 commit 0.99.8
 
    
  
    

      Package: limma

      Commit: 7073db8b7b05e090ee46cebce688ba9b6036f07d

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-08-30 19:54:02 +1000

      Commit message:


	  
		
 More edits to diffSplice.Rd
 
    
  
    

      Package: dupRadar

      Commit: 41f3c82e430f745a8351284c8a82e7a2bdcb4792

      Author:  Sergi Sayols <sergisayolspuig@gmail.com> 

      Date: 2025-08-30 11:02:47 +0200

      Commit message:


	  
		
 feat: add tmpDir parameter to analyzeDuprates
 
    
  
    

      Package: OSTA.data

      Commit: 4c52a2ae27b4aecfefbeb705f20c9b51d550939f

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-08-29 18:12:42 +0200

      Commit message:


	  
		
 update version
 
    
  
    

      Package: OSTA.data

      Commit: f613c376516e2c7dafbe0cd5b2ce419f8086e9be

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-08-29 18:04:57 +0200

      Commit message:


	  
		
 update version
 
    
  
    

      Package: OSTA.data

      Commit: 090321a87b51b04d81ab95cb372f67c5a7493b98

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-08-29 10:06:26 +0200

      Commit message:


	  
		
 update news add sticker
 
    
  
    

      Package: spatialFDA

      Commit: 6b8167f4da7c26323e2a8c48deb740b3f035b4c9

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-08-29 17:40:13 +0200

      Commit message:


	  
		
 mean residuals per condition and min nndist for delta
 
    
  
    

      Package: iSEEtree

      Commit: b1b4d6ebd16d4e53d2a6735fc4991c2a009e6b2f

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2025-08-29 18:35:14 +0300

      Commit message:


	  
		
 Merge pull request #49 from microbiome/testing

Add unit tests for new panels 
    
  
    

      Package: iSEEtree

      Commit: fa98b751b53e13cd9bb0fddf857f70a8a71ffea6

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2025-08-29 17:58:49 +0300

      Commit message:


	  
		
 Add unit tests for new panels
 
    
  
    

      Package: biomaRt

      Commit: 6872436a07010ca664ebafdbfe4813fc0909d5aa

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 16:25:35 +0200

      Commit message:


	  
		
 Simplify setEnsemblSSL with modifyList()
 
    
  
    

      Package: miloR

      Commit: be20c8ba7784b564be3d6e3738194696018b1449

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2025-08-29 14:57:51 +0100

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: miloR

      Commit: cb3216a46bcf204f99a7391e5ca268843a344a96

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2025-08-29 14:51:58 +0100

      Commit message:


	  
		
 fix sporadic error when only 1 sigma is detected because of NA estimates
 
    
  
    

      Package: miloR

      Commit: c1a01b9c1f97d55e54a6d1384532e23c15442cdc

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2025-08-28 18:46:58 +0100

      Commit message:


	  
		
 fix bug in GLMM with multiple random effects including with a GRM
 
    
  
    

      Package: MsBackendSql

      Commit: dc774fe6f804ae42fcbe15829609e34046ef728e

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-08-29 13:50:21 +0200

      Commit message:


	  
		
 Merge pull request #27 from rformassspectrometry/duckdb

feat: add support for duckdb blob2 storage mode 
    
  
    

      Package: MsBackendSql

      Commit: ffa3fc46ec50f61dfcde6403c78af422cc18bc06

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-08-29 13:03:48 +0200

      Commit message:


	  
		
 feat: add support for duckdb blob2 storage mode
 
    
  
    

      Package: biomaRt

      Commit: 772036e4b0fe9da1c657bb47f5ac54529344134d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 12:18:43 +0200

      Commit message:


	  
		
 Make dependency on R 4.5 explicit

Follow up from 7b4e1102fd100e2c5da681276f89750b4028db74
 
    
  
    

      Package: igblastr

      Commit: 07d59d756b634b252c39be1744b8471a079e5833

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 22:44:34 -0700

      Commit message:


	  
		
 small tweaks to README.md
 
    
  
    

      Package: igblastr

      Commit: a0d72e6860bfaa0d1197b8889a52a2b93e7b217e

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 22:34:15 -0700

      Commit message:


	  
		
 igblastr 0.99.14

- More bells and whistles to the README.md file.
- Small improvement to igblastn() examples in man/igblastn.Rd.
- Some internal reorganization of the R/IMGT-utils.R code.
- Update TODO file.
 
    
  
    

      Package: h5mread

      Commit: 519affb2bcfa1452d019bb816fe7aaecb7d12345

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 20:12:22 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 
    
  
    

      Package: S4Arrays

      Commit: acd60e82117b0a8d669da8ddf810add0f0eba07e

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 20:08:25 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 
    
  
    

      Package: HDF5Array

      Commit: d8785db0ba4363f0f8e5f3c2e546b3b3b7f75c0a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 20:03:32 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 
    
  
    

      Package: SparseArray

      Commit: 2dd1bf90ea032006c22fe05149e52b404bfac781

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:55:59 -0700

      Commit message:


	  
		
 try again
 
    
  
    

      Package: SparseArray

      Commit: 95b9508a4a5a339b1a598f76974c6510caa5f4d6

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:52:21 -0700

      Commit message:


	  
		
 try again
 
    
  
    

      Package: SparseArray

      Commit: 1aa154b36349add6f0e0bb0125d044e671cca6fc

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:49:31 -0700

      Commit message:


	  
		
 try again
 
    
  
    

      Package: SparseArray

      Commit: d38de47810a4b772579220abc0508b0722844057

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:48:37 -0700

      Commit message:


	  
		
 try again
 
    
  
    

      Package: SparseArray

      Commit: 47d56ad7a6a07a70f39389ff00763ed4167ca456

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:47:41 -0700

      Commit message:


	  
		
 Try to improve layout of images in README.md
 
    
  
    

      Package: SparseArray

      Commit: c7972f27d40c22375bf4d9ce0645c420e0fb1535

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:44:28 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 
    
  
    

      Package: DelayedArray

      Commit: 21982e41933d0fc4f2464b2282a07080cc65049a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 18:53:06 -0700

      Commit message:


	  
		
 minor improvements to README.md
 
    
  
    

      Package: DelayedArray

      Commit: 2a2cf695f3e3648942dabb1c3b3c2a65513a9856

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 17:55:44 -0700

      Commit message:


	  
		
 tweak layout a little
 
    
  
    

      Package: DelayedArray

      Commit: d65b462b975c28a85fc8de4eb30d30e9481f1f5c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 17:54:21 -0700

      Commit message:


	  
		
 add "build" and "platforms" shields for devel in addition to release
 
    
  
    

      Package: DelayedArray

      Commit: 2825f0c54923d254494d467560a3a5bb10ed82a2

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2025-08-28 20:43:55 -0400

      Commit message:


	  
		
 Tweak README.md for better compatibility with pkgdown (#124)

 
    
  
    

      Package: limma

      Commit: d39d01194a21d91260b8468d98f138871fa332b1

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-08-29 10:13:32 +1000

      Commit message:


	  
		
 limma 3.65.4

- The default for `adaptive.span` in voom() and
  voomWithQualityWeights() is now `TRUE`. All the voom functions now
  use chooseLowessSpan() by default to choose the `span`.

- New argument `xlab` for plotSplice() to allow labeling in terms of
  transcripts or other splicing events instead of exons.

- The help pages for diffSplice(), topSplice() and plotSplice() have
  been updated to emphasize differential transcript usage instead of
  differential exon usage or differential splicing.
 
    
  
    

      Package: iscream

      Commit: 2aac56205878ba39f14d6a39a2c9f45adce65a43

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-08-28 19:10:19 -0400

      Commit message:


	  
		
 test(tabix): skip if tabix is not installed
 
    
  
    

      Package: assorthead

      Commit: dd199372a12a5f851db6a8b0f7e64d67d1211a91

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-08-28 15:11:43 -0700

      Commit message:


	  
		
 Updated the vendored nenesub.
 
    
  
    

      Package: iModMixData

      Commit: 7623b9a35bcc5ba53667afa9d13fd2d5c850b776

      Author:  Isis Narvaez-Bandera <isis.narvaez@upr.edu> 

      Date: 2025-08-28 13:29:27 -0400

      Commit message:


	  
		
 biocViews: ExperimentData, ExpressionData, MassSpectrometryData, ExperimentHub
 
    
  
    

      Package: biomaRt

      Commit: 7b4e1102fd100e2c5da681276f89750b4028db74

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 19:08:06 +0200

      Commit message:


	  
		
 Remove dependencies superseded by new functions in tools (#140)

 
    
  
    

      Package: biomaRt

      Commit: 17bff63203ee6efd7e50e886679ef96ef695e37e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:54:00 +0200

      Commit message:


	  
		
 Add revdep/ to .Rbuildignore
 
    
  
    

      Package: biomaRt

      Commit: 3e4945f36e8189c65a8f20d38af8bfb9777f9339

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:53:27 +0200

      Commit message:


	  
		
 Add revdep working folders in gitignore
 
    
  
    

      Package: Pirat

      Commit: 61999326e7a0673fc477d18c4fe238fa16930123

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-08-28 10:02:55 -0700

      Commit message:


	  
		
 Add channels
 
    
  
    

      Package: punKEGGer

      Commit: d46c8479cb0106588d8ed2fff721b29814276ea1

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-28 11:01:52 -0600

      Commit message:


	  
		
 Fix DESCRIPTION DCF (no leading ')', clean Authors@R) - v0.99.6
 
    
  
    

      Package: Pirat

      Commit: 2bed5c798e1e08732f26c6bbbd519e04c66061b5

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-08-28 09:52:09 -0700

      Commit message:


	  
		
 Change channel & package
 
    
  
    

      Package: spatialFDA

      Commit: 60ac7c86e8b499acc970fa62cc76f7a516018431

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-08-28 17:09:09 +0200

      Commit message:


	  
		
 major change in min threshold to calculate curves on - set to >1 point - print Rsq.adjust
 
    
  
    

      Package: punKEGGer

      Commit: 23de149f42d2b706328b8d7337ada7a314b1418c

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-28 10:31:16 -0600

      Commit message:


	  
		
 Version bump to 0.99.6 (force SPB rebuild)
 
    
  
    

      Package: GSEABase

      Commit: f9e1f78d51fcdf8b87daf79e65492aeef07fd4ca

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-08-28 11:42:23 -0400

      Commit message:


	  
		
 version bump 1.71.1
 
    
  
    

      Package: GSEABase

      Commit: 451a4471f883490ca935e2a8198f9f4d92ec8fcd

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-08-28 11:43:47 -0400

      Commit message:


	  
		
 add ignore files
 
    
  
    

      Package: GSEABase

      Commit: 60aaab4d5fe13311348354db0cd92c59257399c4

      Author:  Copilot <198982749+Copilot@users.noreply.github.com> 

      Date: 2025-08-28 11:37:03 -0400

      Commit message:


	  
		
 Add support for MSigDB mouse collection categories in BroadCollection (#12)

* Add support for MSigDB mouse collection categories

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
 
    
  
    

      Package: GSEABase

      Commit: 8843b908da13c9b6eb6c59334e6de1a0c50d9159

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-08-27 11:07:39 -0400

      Commit message:


	  
		
 add copilot instructions
 
    
  
    

      Package: BiocFileCache

      Commit: 1fc61764ec373e29bb6436fe47551c8a0b0dd974

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-08-28 11:38:51 -0400

      Commit message:


	  
		
 Merge pull request #68 from Bioconductor/trycatch_download

use tryCatch for bfcdownload when resource is unreliable 
    
  
    

      Package: BiocFileCache

      Commit: d4b686589269ca2e02e84db532ed5b137b8d4311

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-08-27 12:46:25 -0400

      Commit message:


	  
		
 use tryCatch for bfcdownload when resource is unreliable
 
    
  
    

      Package: mzR

      Commit: 7a0319adc132af38fdcdc22e57d1e521dfa67abe

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2025-08-28 15:26:28 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: mzR

      Commit: f04857874fa81bccdbc9edd8171709e889ec1b19

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-15 16:46:30 +0200

      Commit message:


	  
		
 ignore more NaNs
 
    
  
    

      Package: mzR

      Commit: bcb82e383a618a7bc3d66a20ecbdc32ade625b18

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-15 08:44:08 +0200

      Commit message:


	  
		
 ignore more NaNs
 
    
  
    

      Package: mzR

      Commit: b97523ca6318bbe5bbd983a25283fd89030ff560

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-14 17:11:32 +0200

      Commit message:


	  
		
 ignore nan energies
 
    
  
    

      Package: mzR

      Commit: c24f9afdef20987cba491e0cc8eee8a4bb5c8332

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-14 12:58:41 +0200

      Commit message:


	  
		
 add `electronBeamEnergy`
 
    
  
    

      Package: mzR

      Commit: 27c8edb42604522358b18573bda0c10ac88f78f9

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-14 07:51:51 +0200

      Commit message:


	  
		
 ran `updateCvParams.sh`
 
    
  
    

      Package: mzR

      Commit: 0e6f9e9d42c1112e2a6a78e1216d7c3d473d7f71

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2025-08-12 22:37:39 +0200

      Commit message:


	  
		
 Merge pull request #309 from sneumann/sneumann-patch-5

Bump BioC Versions in github action
Fixes GH actions failure on Linux 
    
  
    

      Package: mzR

      Commit: a9041f108127ccb2ed0908299bc8cc23883c7ec5

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2025-08-12 22:04:15 +0200

      Commit message:


	  
		
 Bump BioC Versions in github action 
    
  
    

      Package: tximportData

      Commit: 04d30a42107dcd5e68444e1143520f84764376f2

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-08-28 08:12:34 -0400

      Commit message:


	  
		
 update number of novel in oarfish
 
    
  
    

      Package: msa

      Commit: 72ebbc23c46e5938093565e72fa39662c1970041

      Author:  Ulrich Bodenhofer <ulrichbodenhofer@TAMMISAARI.local> 

      Date: 2025-08-28 13:38:53 +0200

      Commit message:


	  
		
 fixed compilations problems for arm64; version number bumped to 1.41.1
 
    
  
    

      Package: Rarr

      Commit: 3fb74aaeeffb45be70f601e7daab3ed108d02722

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:44:55 +0200

      Commit message:


	  
		
 Fix rchk PROTECT issues (#40)

 
    
  
    

      Package: Rarr

      Commit: d944a2efd2c735577773db11563e89b79990a790

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:42:34 +0200

      Commit message:


	  
		
 Add note in README about lack of v3 support (#41)

 
    
  
    

      Package: Rarr

      Commit: 219dcad29b3aca5d662d44c629832c1fed8705ec

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 09:18:17 +0200

      Commit message:


	  
		
 Use readBin() on a connection (#36)

 
    
  
    

      Package: Rarr

      Commit: ed3c844ce39ebb96f47760d55bd1884ad05be323

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 08:17:51 +0200

      Commit message:


	  
		
 Set up r-hub to test on more uncommon platforms (#38)

 
    
  
  


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