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/1b7ab2684e3277_8147"
## WT
## "/home/biocbuild/.cache/R/ExperimentHub/1b7ab229e11176_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/337fb415d6d53b_8168"
## LIMA_0030
## "/home/biocbuild/.cache/R/ExperimentHub/337fb423cb83f6_8169"
## LIMA_0060
## "/home/biocbuild/.cache/R/ExperimentHub/337fb4a9c0369_8170"
## LIMA_0090
## "/home/biocbuild/.cache/R/ExperimentHub/337fb44d87f8da_8171"
## LIMA_0120
## "/home/biocbuild/.cache/R/ExperimentHub/337fb480364ad_8172"
## LIMA_0240
## "/home/biocbuild/.cache/R/ExperimentHub/337fb449ab8511_8173"
## LIMA_0360
## "/home/biocbuild/.cache/R/ExperimentHub/337fb453672033_8174"
## LIMA_1440
## "/home/biocbuild/.cache/R/ExperimentHub/337fb47f3173e7_8175"sessionInfo()## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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.3.12.0
##
## 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_1.6.0
##
## 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_2.3.7
## [7] digest_0.6.37 magrittr_2.0.3 evaluate_1.0.1
## [10] fastmap_1.2.0 blob_1.2.4 AnnotationHub_3.14.0
## [13] jsonlite_1.8.9 AnnotationDbi_1.68.0 GenomeInfoDb_1.42.0
## [16] DBI_1.2.3 BiocManager_1.30.25 httr_1.4.7
## [19] purrr_1.0.2 fansi_1.0.6 UCSC.utils_1.2.0
## [22] Biostrings_2.74.0 jquerylib_0.1.4 cli_3.6.3
## [25] crayon_1.5.3 rlang_1.1.4 XVector_0.46.0
## [28] dbplyr_2.5.0 Biobase_2.66.0 bit64_4.5.2
## [31] withr_3.0.2 cachem_1.1.0 yaml_2.3.10
## [34] tools_4.4.1 memoise_2.0.1 dplyr_1.1.4
## [37] GenomeInfoDbData_1.2.13 filelock_1.0.3 ExperimentHub_2.14.0
## [40] BiocGenerics_0.52.0 curl_5.2.3 mime_0.12
## [43] png_0.1-8 vctrs_0.6.5 R6_2.5.1
## [46] stats4_4.4.1 BiocFileCache_2.14.0 lifecycle_1.0.4
## [49] zlibbioc_1.52.0 KEGGREST_1.46.0 S4Vectors_0.44.0
## [52] IRanges_2.40.0 bit_4.5.0 pkgconfig_2.0.3
## [55] pillar_1.9.0 bslib_0.8.0 glue_1.8.0
## [58] xfun_0.48 tibble_3.2.1 tidyselect_1.2.1
## [61] knitr_1.48 htmltools_0.5.8.1 rmarkdown_2.28
## [64] compiler_4.4.1