3464b6f1b3126a020057e91b4baf06c0 *DESCRIPTION
d200ecfdc439a3867b1632deac013b13 *NAMESPACE
3275c83c00dda743f8249059a19544d8 *NEWS
61616a27a19461f6308aa2852130cac2 *R/CV_calculation.R
f65287f750e4dbf79bf7d41d28756e3a *R/ProBatchFeatures.R
79c34722a2736c624acdf4809f6118c7 *R/auxiliary.R
b86e1be1412e10fbf63c806e52a027c1 *R/colors_for_annotation.R
aa54b1bc9b2af171726082d128060e4e *R/correct_batch_effects.R
819ac8c4f4851f9ce3289a898a187ed1 *R/correlation-based_diagnostics.R
a5e2ac9cd2363c4eaf8ea66e06778bde *R/data.R
49cbddc1417193feeb2b4e90b6ae1972 *R/date_conversion.R
d8d4b5e72d9f12c3ff537aa873d044cb *R/feature_level_diagnostics.R
dd90c23882e43665a22b70db22da06d2 *R/fit_non_linear.R
096da4f29a9b84655a8c12e81f8cf1c4 *R/handle_missing_values.R
b9888c22ccb45487b4df7a0dea51b04a *R/initial_assessment.R
bba011835a93e547b08154b003a38c8c *R/normalize.R
85b475f6d748661159ccb79de02e5b52 *R/pb_missing_filters.R
ab2eef1deb3a1147d00e02d14cccc6a8 *R/plot_helpers.R
97e02ad1aef472eb55d616b7166cb417 *R/plot_missing.R
862318f0cf6a05b326ac9c47e3baeba1 *R/plot_split_violinplot.R
7e8874f0a72dfb6abe88ac621c57e0fd *R/proBatch.R
fd8f810386f8734a20835c2ba0fa093c *R/proteome_wide_diagnostics.R
a882ee4276f4592f86ab0da972290098 *R/transform_raw.R
079ac4a1fbed95ef6932100edc1cd72d *R/utility_funcs.R
69e5dea8aef9a93e3797d0145f6dcd9f *R/zzz_helpers.R
0a20f76bd0fcc809034b526a0db04cbc *README.md
9f0b4de6ec1a4aca3e349e904a368298 *build/vignette.rds
8cf8cd352b50e940a6581c266886d19e *data/datalist
5c5c366e1170864eedf8643621b41164 *data/example_ecoli_data.rda
5987bc06870b38f89e0d49a0d59d641b *data/example_peptide_annotation.rda
bad3339ab13ce311beeacbe71d11dc98 *data/example_proteome.rda
615248cfecb89b8953cceba9f985c017 *data/example_proteome_matrix.rda
7fd3d91f7f5c6db40c1f91577f69a059 *data/example_sample_annotation.rda
dd552bbda624bcbb8566417547afe24b *inst/CITATION
f9ec7d2ca40e9e41f14cddd853b26986 *inst/WORDLIST
a11e09a1a18ad26945c3a2ced074a56a *inst/doc/proBatch.R
52a9c2770a741666bd1a4a99a9840ecf *inst/doc/proBatch.Rmd
a07f5ab4a5148a2f5815a454c8d0bf42 *inst/doc/proBatch.html
af42d4f1bbda6647a9551cbabbf17443 *inst/doc/proBatchFeatures.R
4eaf9d11328502793a3d8331921bc674 *inst/doc/proBatchFeatures.Rmd
7a861cb00635213e0ff89078b85a6d09 *inst/doc/proBatchFeatures.html
f23ba350521adad60281ce920da1e36e *inst/examples/ProBatchFeatures-basic.R
cb662b71deeb30904c50440eb6e359bb *man/ProBatchFeatures-class.Rd
4687d0a41e763abd2568c3dce0d2c8bf *man/ProBatchFeatures-subset.Rd
acff38b29cf482dac256dedaa4cb83ef *man/ProBatchFeatures.Rd
cb7fcde9328c9483a4251b936416ba24 *man/ProBatchFeatures_from_long.Rd
e998710d44fc3961290380583fd65b14 *man/calculate_PVCA.Rd
8481b5db3991c42d85c747b4e0acfd6d *man/calculate_feature_CV.Rd
83c6776ec93626a02671edd43e236771 *man/calculate_peptide_corr_distr.Rd
0bb7024c73ab5d13de31813c4c6ed25b *man/calculate_sample_corr_distr.Rd
9356088ddbda34cea51ccc947f7c0319 *man/check_sample_consistency.Rd
52fd514f2f8de8931f115443f836c949 *man/color_list_to_df.Rd
66241c9492f823dbcafe3eb5343ffd96 *man/convert_annotation_classes.Rd
f0ee8946d910c3682fc38f5ca8119a28 *man/correct_batch_effects.Rd
10211142cf3eb2f029020b1f3307b94d *man/correct_with_removeBatchEffect_dm.Rd
ec4568b13c4db33457bb8d3a15d2e756 *man/create_peptide_annotation.Rd
43a07a99083f8d2a875b60595360bf44 *man/date_to_sample_order.Rd
d66127b5b8ffa5add010aa17f3de7c88 *man/dates_to_posix.Rd
dba067900f44695457cc6ee71dfe7f8a *man/define_sample_order.Rd
1e90eed1031aa5ef9da54b82f799ecad *man/example_ecoli_data.Rd
f26f08503486f5d799152670ecf03a1e *man/example_peptide_annotation.Rd
bd5e854d3637218934f54627d254192c *man/example_proteome.Rd
73095a94166a0b1edadf42839a9649b2 *man/example_proteome_matrix.Rd
414556685d561e259333c4f9faf74b75 *man/example_sample_annotation.Rd
ec03a94288dc7469a4b611f74ed961f5 *man/feature_level_diagnostics.Rd
46ea4d0e1f9f3af2d9fe148e6272ea59 *man/fit_nonlinear.Rd
5a69a86879c4b43016d75f87311aabc4 *man/generate_colors_for_numeric.Rd
59bacb10bbc3f1a6e71e68c6f194577b *man/get_chain.Rd
39ab11fc020d9b003ac47d7cae2e6771 *man/get_operation_log.Rd
cec8b2b3c5174590073c415b17e25627 *man/guess_factor_columns_if_needed.Rd
fc672b3630166aca2fa31da1d41e4cc7 *man/handle_factor_numeric_overlap.Rd
fb5693d23d59f52d5e21fe5df265323d *man/handle_missing_values.Rd
93dfe5285dcaf300dc2094ce791eb756 *man/long_to_matrix.Rd
476b4e5019895fca9a0cbfcaa4782579 *man/matrix_to_long.Rd
1674c3655faf08ec73eb64404fffc4aa *man/merge_rare_levels.Rd
8bbadcb54930782b1f1b7213c72c00aa *man/normalize.Rd
6620a8bda58d8174d5fbe2e950798f6f *man/pb_add_level.Rd
994271b56dddbb6f8bc935cecf7e6727 *man/pb_aggregate_level.Rd
64a09e85ac5d86c4c27b5ed5e4abaf8c *man/pb_as_long.Rd
4a95d6e2d0f5021f87ecf0caaa3c6730 *man/pb_as_wide.Rd
c614e2f1705b57a6f35b206d27990e75 *man/pb_assay_matrix.Rd
9b59c574129485a19b06c4396803bf44 *man/pb_current_assay.Rd
4f9f8bb4f7a04c07b714f73ede00f3f7 *man/pb_eval.Rd
9b8168c4f7b49cd8cb62d6bad1f88522 *man/pb_missing_helpers.Rd
d0ee58df778f508a8432af7b54b5840f *man/pb_pipeline_name.Rd
4aa23d2a12a24dcb4ddbdea3ed5d2979 *man/pb_register_step.Rd
429e8cd0598ebffaca410eff2861db09 *man/pb_transform.Rd
55910eba11d578076d87e4901bf70586 *man/plot_CV_distr.Rd
72ea5b0e73c332e02f0291e6a7f746d9 *man/plot_CV_distr.df.Rd
5ee23f92f38f8aa7bbd69a17f0f6719c *man/plot_NA_density.Rd
7011dd3d46a31e4e56629f8f9bf4be4f *man/plot_NA_frequency.Rd
6a825af55f1e06d95ad8ca494c4191d4 *man/plot_NA_heatmap.Rd
708a4240926f9ecdaab031818d43dd7b *man/plot_PCA.Rd
e3db2d7152b663126f1672d110ac0118 *man/plot_PVCA.Rd
4b9c72149861e4ff1babea8c7fc9ba3b *man/plot_PVCA.df.Rd
b4597702a0dbc2d143b0a6137db7d55c *man/plot_corr_matrix.Rd
2491ec927dde538fa8c139835b97ba86 *man/plot_heatmap_diagnostic.Rd
b3f1c6f71fc7c2b4e5fab10d5feb29e1 *man/plot_heatmap_generic.Rd
6b3f730acb375f02c9c52bfc4d973415 *man/plot_hierarchical_clustering.Rd
96d1a940e029b07e97a2299792bc10c1 *man/plot_peptide_corr_distribution.Rd
dee3433b3a3033d0c14c4653756aca36 *man/plot_protein_corrplot.Rd
a2ed7f814bd7dcd27a1d2636cc705f73 *man/plot_sample_corr_distribution.Rd
59d3a9b242794cbecc76eb4b3fbfdde0 *man/plot_sample_corr_heatmap.Rd
e4e8ded124cd494421f5fbfeeb2ec89d *man/plot_sample_mean_or_boxplot.Rd
c93ecdfae315394a3d6143d0376b1f1b *man/plot_split_violin_with_boxplot.Rd
b01e5d4c9f7b63e9b6b75e00f2e488b1 *man/prepare_PVCA_df.Rd
59c964bbd1752ca1e2e531643323b41c *man/proBatch.Rd
dd0af35691ccdca2f0ec9a43ac079989 *man/sample_annotation_to_colors.Rd
76a8b2a98846a75c0e69581b46af1dff *man/subset_keep_cols.Rd
e3ee71d204556c4067eccd720659fb75 *man/transform_raw_data.Rd
ce7502e9da3e78bec4bbc0f81530aee0 *man/warn_unmapped_columns.Rd
92262a20660ecace2cb8c021a5bb49f7 *tests/spelling.R
b6fecab3fc35fc8e5e1f35414122082f *tests/testthat.R
f11585667b104f3ee05f65d27cace879 *tests/testthat/test-CV_calculation.R
9dca5f9dd3da556ea1501d923c9fc4ff *tests/testthat/test-ProBatchFeatures.R
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afbbcd6470572c2b7a46e4f57524ee95 *tests/testthat/test-batch_effect_steps.R
4918967eefbbb5bbd78b95838466a366 *tests/testthat/test-colors_for_annotation.R
8f9e74538df8f3100996d2df4a8fdc60 *tests/testthat/test-correct_batch_effect.R
3bb966dde1493ca356f0af0288da1d1d *tests/testthat/test-correlation_based_diagnostics.R
a9cb2aeead2770f0e2c799bceccc9957 *tests/testthat/test-date_conversion.R
43c1e380c353774706b85040def24f93 *tests/testthat/test-feature_level_diagnostics.R
6a8c729b84a7ae6df368207bd0378ed4 *tests/testthat/test-fit_non_linear.R
457cb51d06533f4a796a5d73c6eb1258 *tests/testthat/test-handle_missing_values.R
4ca745c178232812d25899da982d492a *tests/testthat/test-initial_assessment.R
c3f1eb8242b98ccf34a13d05f76e96f1 *tests/testthat/test-normalize.R
b089ff73b7b461a624781b332ef1421f *tests/testthat/test-pb_missing_helpers.R
01136a4d4be843407e7d41087907a680 *tests/testthat/test-plot_missing.R
851bec5f4e4476d4df8cc1a0dffa39fe *tests/testthat/test-plot_split_violinplot.R
6c8832b0d2d8ae172b7e8467ec0aa19a *tests/testthat/test-proteome_wide_diagnostics.R
578b1ed0239ddf59c02af7a0e409dc19 *tests/testthat/test-transform_raw.R
5e02458403ac9ed7d2c2655d0e32f8d5 *tests/testthat/test-utility_funcs.R
b1ef32672b71e1e98433beac3e247f6c *vignettes/Batch_effects_workflow_staircase.png
56606261434aaedb423f23684e15e316 *vignettes/nature-no-superscript.csl
52a9c2770a741666bd1a4a99a9840ecf *vignettes/proBatch.Rmd
4eaf9d11328502793a3d8331921bc674 *vignettes/proBatchFeatures.Rmd
394c41b861fbcf753fd98118e9930892 *vignettes/pvca_quantile_normalized.png
9d4bc7b98eaf28bdb367a66197ffe105 *vignettes/references.bib
