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/1ea5e5a3c502e_8147"
## WT
## "/home/biocbuild/.cache/R/ExperimentHub/1ea5e552176755_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/254693661e2c3b_8168"
## LIMA_0030
## "/home/biocbuild/.cache/R/ExperimentHub/254693591a9c29_8169"
## LIMA_0060
## "/home/biocbuild/.cache/R/ExperimentHub/254693485a1ac8_8170"
## LIMA_0090
## "/home/biocbuild/.cache/R/ExperimentHub/25469359ff680c_8171"
## LIMA_0120
## "/home/biocbuild/.cache/R/ExperimentHub/254693676f94b4_8172"
## LIMA_0240
## "/home/biocbuild/.cache/R/ExperimentHub/254693357c928_8173"
## LIMA_0360
## "/home/biocbuild/.cache/R/ExperimentHub/2546932b8c19b6_8174"
## LIMA_1440
## "/home/biocbuild/.cache/R/ExperimentHub/25469373e58547_8175"sessionInfo()## R version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-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_1.4.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3 sass_0.4.9 utf8_1.2.4
## [4] generics_0.1.3 BiocVersion_3.19.1 RSQLite_2.3.6
## [7] digest_0.6.35 magrittr_2.0.3 evaluate_0.23
## [10] fastmap_1.1.1 blob_1.2.4 AnnotationHub_3.12.0
## [13] jsonlite_1.8.8 AnnotationDbi_1.66.0 GenomeInfoDb_1.40.0
## [16] DBI_1.2.2 BiocManager_1.30.22 httr_1.4.7
## [19] purrr_1.0.2 fansi_1.0.6 UCSC.utils_1.0.0
## [22] Biostrings_2.72.0 jquerylib_0.1.4 cli_3.6.2
## [25] crayon_1.5.2 rlang_1.1.3 XVector_0.44.0
## [28] dbplyr_2.5.0 Biobase_2.64.0 bit64_4.0.5
## [31] withr_3.0.0 cachem_1.0.8 yaml_2.3.8
## [34] tools_4.4.0 memoise_2.0.1 dplyr_1.1.4
## [37] GenomeInfoDbData_1.2.12 filelock_1.0.3 ExperimentHub_2.12.0
## [40] BiocGenerics_0.50.0 curl_5.2.1 mime_0.12
## [43] png_0.1-8 vctrs_0.6.5 R6_2.5.1
## [46] stats4_4.4.0 BiocFileCache_2.12.0 lifecycle_1.0.4
## [49] zlibbioc_1.50.0 KEGGREST_1.44.0 S4Vectors_0.42.0
## [52] IRanges_2.38.0 bit_4.0.5 pkgconfig_2.0.3
## [55] pillar_1.9.0 bslib_0.7.0 glue_1.7.0
## [58] xfun_0.43 tibble_3.2.1 tidyselect_1.2.1
## [61] knitr_1.46 htmltools_0.5.8.1 rmarkdown_2.26
## [64] compiler_4.4.0