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 cache
names(hicFiles) <- c("FS", "WT")
hicFiles
## FS
## "/home/biocbuild/.cache/R/ExperimentHub/2a3ec81693dced_8147"
## WT
## "/home/biocbuild/.cache/R/ExperimentHub/2a3ec8d002731_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 cache
Additionally, 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 cache
names(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/1459124bf1a05d_8168"
## LIMA_0030
## "/home/biocbuild/.cache/R/ExperimentHub/145912539426cb_8169"
## LIMA_0060
## "/home/biocbuild/.cache/R/ExperimentHub/145912466adc0a_8170"
## LIMA_0090
## "/home/biocbuild/.cache/R/ExperimentHub/145912326fde57_8171"
## LIMA_0120
## "/home/biocbuild/.cache/R/ExperimentHub/1459126d078f3b_8172"
## LIMA_0240
## "/home/biocbuild/.cache/R/ExperimentHub/14591247f4240d_8173"
## LIMA_0360
## "/home/biocbuild/.cache/R/ExperimentHub/1459127faab72f_8174"
## LIMA_1440
## "/home/biocbuild/.cache/R/ExperimentHub/14591229daa295_8175"
sessionInfo()
## R version 4.4.0 RC (2024-04-16 r86468)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.20-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_1.5.0
##
## 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_3.20.0 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_3.13.0
## [13] jsonlite_1.8.8 AnnotationDbi_1.67.0 GenomeInfoDb_1.41.0
## [16] DBI_1.2.2 BiocManager_1.30.22 httr_1.4.7
## [19] purrr_1.0.2 fansi_1.0.6 UCSC.utils_1.1.0
## [22] Biostrings_2.73.0 jquerylib_0.1.4 cli_3.6.2
## [25] crayon_1.5.2 rlang_1.1.3 XVector_0.45.0
## [28] dbplyr_2.5.0 Biobase_2.65.0 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_2.13.0
## [40] BiocGenerics_0.51.0 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_2.13.0 lifecycle_1.0.4
## [49] zlibbioc_1.51.0 KEGGREST_1.45.0 S4Vectors_0.43.0
## [52] IRanges_2.39.0 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