The marinerData package provides some small Hi-C files for the mariner package vignettes and tests.
library(marinerData)
hicFiles <- 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/1824d4781a1436_8147"
## WT
## "/home/biocbuild/.cache/R/ExperimentHub/1824d470442ea8_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/23c2d263c574cb_8168"
## LIMA_0030
## "/home/biocbuild/.cache/R/ExperimentHub/23c2d25d62810e_8169"
## LIMA_0060
## "/home/biocbuild/.cache/R/ExperimentHub/23c2d2c2bfc95_8170"
## LIMA_0090
## "/home/biocbuild/.cache/R/ExperimentHub/23c2d273f448d5_8171"
## LIMA_0120
## "/home/biocbuild/.cache/R/ExperimentHub/23c2d2588e2089_8172"
## LIMA_0240
## "/home/biocbuild/.cache/R/ExperimentHub/23c2d255e178b7_8173"
## LIMA_0360
## "/home/biocbuild/.cache/R/ExperimentHub/23c2d2495943d6_8174"
## LIMA_1440
## "/home/biocbuild/.cache/R/ExperimentHub/23c2d25ce0039e_8175"sessionInfo()## R version 4.5.0 beta (2025-04-02 r88102)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-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_1.9.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3 sass_0.4.10 generics_0.1.3
## [4] BiocVersion_3.22.0 RSQLite_2.3.9 digest_0.6.37
## [7] magrittr_2.0.3 evaluate_1.0.3 fastmap_1.2.0
## [10] blob_1.2.4 AnnotationHub_3.17.0 jsonlite_2.0.0
## [13] AnnotationDbi_1.71.0 GenomeInfoDb_1.45.0 DBI_1.2.3
## [16] BiocManager_1.30.25 httr_1.4.7 purrr_1.0.4
## [19] UCSC.utils_1.5.0 Biostrings_2.77.0 jquerylib_0.1.4
## [22] cli_3.6.4 rlang_1.1.6 crayon_1.5.3
## [25] XVector_0.49.0 dbplyr_2.5.0 Biobase_2.69.0
## [28] bit64_4.6.0-1 withr_3.0.2 cachem_1.1.0
## [31] yaml_2.3.10 tools_4.5.0 memoise_2.0.1
## [34] dplyr_1.1.4 GenomeInfoDbData_1.2.14 filelock_1.0.3
## [37] ExperimentHub_2.17.0 BiocGenerics_0.55.0 curl_6.2.2
## [40] mime_0.13 vctrs_0.6.5 R6_2.6.1
## [43] png_0.1-8 stats4_4.5.0 BiocFileCache_2.17.0
## [46] lifecycle_1.0.4 KEGGREST_1.49.0 S4Vectors_0.47.0
## [49] IRanges_2.43.0 bit_4.6.0 pkgconfig_2.0.3
## [52] pillar_1.10.2 bslib_0.9.0 glue_1.8.0
## [55] xfun_0.52 tibble_3.2.1 tidyselect_1.2.1
## [58] knitr_1.50 htmltools_0.5.8.1 rmarkdown_2.29
## [61] compiler_4.5.0