The marinerData package provides some small Hi-C files for the mariner package vignettes and tests.
library(marinerData)## Warning: replacing previous import 'utils::findMatches' by
## 'S4Vectors::findMatches' when loading 'AnnotationDbi'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/211a9b571fe228_8147"
## WT
## "/home/biocbuild/.cache/R/ExperimentHub/211a9b766098f9_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/211a9b4d4e577a_8168"
## LIMA_0030
## "/home/biocbuild/.cache/R/ExperimentHub/211a9b26a0036b_8169"
## LIMA_0060
## "/home/biocbuild/.cache/R/ExperimentHub/211a9ba5f87af_8170"
## LIMA_0090
## "/home/biocbuild/.cache/R/ExperimentHub/211a9bf7d4f95_8171"
## LIMA_0120
## "/home/biocbuild/.cache/R/ExperimentHub/211a9b4648de5a_8172"
## LIMA_0240
## "/home/biocbuild/.cache/R/ExperimentHub/211a9b3bb784d0_8173"
## LIMA_0360
## "/home/biocbuild/.cache/R/ExperimentHub/211a9b65dfe47e_8174"
## LIMA_1440
## "/home/biocbuild/.cache/R/ExperimentHub/211a9b2950c931_8175"sessionInfo()## R version 4.3.0 RC (2023-04-13 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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_1.0.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.40.0 xfun_0.39
## [3] bslib_0.4.2 Biobase_2.60.0
## [5] bitops_1.0-7 vctrs_0.6.2
## [7] tools_4.3.0 generics_0.1.3
## [9] stats4_4.3.0 curl_5.0.0
## [11] tibble_3.2.1 fansi_1.0.4
## [13] AnnotationDbi_1.62.0 RSQLite_2.3.1
## [15] blob_1.2.4 pkgconfig_2.0.3
## [17] dbplyr_2.3.2 S4Vectors_0.38.0
## [19] GenomeInfoDbData_1.2.10 lifecycle_1.0.3
## [21] compiler_4.3.0 Biostrings_2.68.0
## [23] GenomeInfoDb_1.36.0 httpuv_1.6.9
## [25] htmltools_0.5.5 sass_0.4.5
## [27] RCurl_1.98-1.12 yaml_2.3.7
## [29] interactiveDisplayBase_1.38.0 pillar_1.9.0
## [31] later_1.3.0 crayon_1.5.2
## [33] jquerylib_0.1.4 ellipsis_0.3.2
## [35] cachem_1.0.7 mime_0.12
## [37] ExperimentHub_2.8.0 AnnotationHub_3.8.0
## [39] tidyselect_1.2.0 digest_0.6.31
## [41] purrr_1.0.1 dplyr_1.1.2
## [43] BiocVersion_3.17.1 fastmap_1.1.1
## [45] cli_3.6.1 magrittr_2.0.3
## [47] utf8_1.2.3 withr_2.5.0
## [49] filelock_1.0.2 promises_1.2.0.1
## [51] rappdirs_0.3.3 bit64_4.0.5
## [53] rmarkdown_2.21 XVector_0.40.0
## [55] httr_1.4.5 bit_4.0.5
## [57] png_0.1-8 memoise_2.0.1
## [59] shiny_1.7.4 evaluate_0.20
## [61] knitr_1.42 IRanges_2.34.0
## [63] BiocFileCache_2.8.0 rlang_1.1.0
## [65] Rcpp_1.0.10 xtable_1.8-4
## [67] glue_1.6.2 DBI_1.1.3
## [69] BiocManager_1.30.20 BiocGenerics_0.46.0
## [71] jsonlite_1.8.4 R6_2.5.1
## [73] zlibbioc_1.46.0