The marinerData package provides some small Hi-C files for the mariner package vignettes and tests.
library(marinerData)## Registered S3 method overwritten by 'bit64':
## method from
## print.bitstring toolshicFiles <- c(
LEUK_HEK_PJA27_inter_30.hic(),
LEUK_HEK_PJA30_inter_30.hic()
)## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cachenames(hicFiles) <- c("FS", "WT")
hicFiles## FS
## "/home/biocbuild/.cache/R/ExperimentHub/801e65772bc2f_8147"
## WT
## "/home/biocbuild/.cache/R/ExperimentHub/801e64ff0f19d_8148"It also provides two sets of loop calls. The following two files correspond to the test Hi-C files described above.
library(marinerData)
nha9Loops <- c(
FS_5kbLoops.txt(),
WT_5kbLoops.txt()
)## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cacheAdditionally, loop calls from a THP-1 activation timecourse are also provided. These cells were exposed to LPS & IF-G for 0, 30, 60, 90, 120, 240, 360, or 1440 minutes. The dataset is abbreviated as LIMA (LPS/IF-G Induced Macrophage Activation).
library(marinerData)
limaLoops <- c(
LIMA_0000.bedpe(),
LIMA_0030.bedpe(),
LIMA_0060.bedpe(),
LIMA_0090.bedpe(),
LIMA_0120.bedpe(),
LIMA_0240.bedpe(),
LIMA_0360.bedpe(),
LIMA_1440.bedpe()
)## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## loading from cachenames(limaLoops) <- c(
"LIMA_0000",
"LIMA_0030",
"LIMA_0060",
"LIMA_0090",
"LIMA_0120",
"LIMA_0240",
"LIMA_0360",
"LIMA_1440"
)
limaLoops## LIMA_0000
## "/home/biocbuild/.cache/R/ExperimentHub/200d775d2a7fdf_8168"
## LIMA_0030
## "/home/biocbuild/.cache/R/ExperimentHub/200d773695a6bc_8169"
## LIMA_0060
## "/home/biocbuild/.cache/R/ExperimentHub/200d7776c572bb_8170"
## LIMA_0090
## "/home/biocbuild/.cache/R/ExperimentHub/200d772a7e8dc3_8171"
## LIMA_0120
## "/home/biocbuild/.cache/R/ExperimentHub/200d7732bd1938_8172"
## LIMA_0240
## "/home/biocbuild/.cache/R/ExperimentHub/200d7757eaebd5_8173"
## LIMA_0360
## "/home/biocbuild/.cache/R/ExperimentHub/200d775c7ea7cd_8174"
## LIMA_1440
## "/home/biocbuild/.cache/R/ExperimentHub/200d77188a045c_8175"sessionInfo()## R version 4.6.0 RC (2026-04-17 r89917)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] marinerData_1.11.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.4 sass_0.4.10 generics_0.1.4
## [4] BiocVersion_3.23.1 RSQLite_2.4.6 digest_0.6.39
## [7] magrittr_2.0.5 evaluate_1.0.5 fastmap_1.2.0
## [10] blob_1.3.0 AnnotationHub_4.1.0 jsonlite_2.0.0
## [13] AnnotationDbi_1.73.1 DBI_1.3.0 BiocManager_1.30.27
## [16] httr_1.4.8 purrr_1.2.2 Biostrings_2.79.5
## [19] httr2_1.2.2 jquerylib_0.1.4 cli_3.6.6
## [22] crayon_1.5.3 rlang_1.2.0 XVector_0.51.0
## [25] dbplyr_2.5.2 Biobase_2.71.0 bit64_4.6.0-1
## [28] withr_3.0.2 cachem_1.1.0 yaml_2.3.12
## [31] otel_0.2.0 tools_4.6.0 memoise_2.0.1
## [34] dplyr_1.2.1 filelock_1.0.3 ExperimentHub_3.1.0
## [37] BiocGenerics_0.57.1 curl_7.0.0 vctrs_0.7.3
## [40] R6_2.6.1 png_0.1-9 stats4_4.6.0
## [43] BiocFileCache_3.1.0 lifecycle_1.0.5 Seqinfo_1.1.0
## [46] KEGGREST_1.51.1 S4Vectors_0.49.2 IRanges_2.45.0
## [49] bit_4.6.0 pkgconfig_2.0.3 pillar_1.11.1
## [52] bslib_0.10.0 glue_1.8.1 xfun_0.57
## [55] tibble_3.3.1 tidyselect_1.2.1 knitr_1.51
## [58] htmltools_0.5.9 rmarkdown_2.31 compiler_4.6.0