The marinerData package provides some small Hi-C files for the mariner package vignettes and tests.
## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## FS
## "/github/home/.cache/R/ExperimentHub/13cd34e2f592_8147"
## WT
## "/github/home/.cache/R/ExperimentHub/13cd2fb986dd_8148"It also provides two sets of loop calls. The following two files correspond to the test Hi-C files described above.
## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## 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## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## see ?marinerData and browseVignettes('marinerData') for documentation## downloading 1 resources## retrieving 1 resource## Error while performing HEAD request.
## Proceeding without cache information.## loading from cachenames(limaLoops) <- c(
"LIMA_0000",
"LIMA_0030",
"LIMA_0060",
"LIMA_0090",
"LIMA_0120",
"LIMA_0240",
"LIMA_0360",
"LIMA_1440"
)
limaLoops## LIMA_0000
## "/github/home/.cache/R/ExperimentHub/13cd58718d05_8168"
## LIMA_0030
## "/github/home/.cache/R/ExperimentHub/13cd6ee5bd58_8169"
## LIMA_0060
## "/github/home/.cache/R/ExperimentHub/13cd46b6045f_8170"
## LIMA_0090
## "/github/home/.cache/R/ExperimentHub/13cddbac5ff_8171"
## LIMA_0120
## "/github/home/.cache/R/ExperimentHub/13cd5c7d47b4_8172"
## LIMA_0240
## "/github/home/.cache/R/ExperimentHub/13cd2dfc9fc9_8173"
## LIMA_0360
## "/github/home/.cache/R/ExperimentHub/13cd417b1a9_8174"
## LIMA_1440
## "/github/home/.cache/R/ExperimentHub/13cd41ee5558_8175"## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] marinerData_1.13.1 rmarkdown_2.32
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.4 sass_0.4.10 generics_0.1.4
## [4] BiocVersion_3.24.0 RSQLite_3.53.3 digest_0.6.39
## [7] magrittr_2.0.5 evaluate_1.0.5 fastmap_1.2.0
## [10] blob_1.3.0 AnnotationHub_4.3.2 jsonlite_2.0.0
## [13] AnnotationDbi_1.75.2 DBI_1.3.0 BiocManager_1.30.27
## [16] httr_1.4.9 purrr_1.2.2 Biostrings_2.81.9
## [19] httr2_1.3.0 jquerylib_0.1.4 cli_3.6.6
## [22] crayon_1.5.3 rlang_1.3.0 XVector_0.53.0
## [25] dbplyr_2.6.0 Biobase_2.73.2 bit64_4.8.6
## [28] withr_3.0.3 cachem_1.1.0 yaml_2.3.12
## [31] BiocBaseUtils_1.15.1 otel_0.2.0 tools_4.6.1
## [34] memoise_2.0.1 dplyr_1.2.1 filelock_1.0.3
## [37] ExperimentHub_3.3.2 BiocGenerics_0.59.12 curl_8.0.0
## [40] png_0.1-9 buildtools_1.0.0 vctrs_0.7.3
## [43] R6_2.6.1 stats4_4.6.1 BiocFileCache_3.3.0
## [46] lifecycle_1.0.5 Seqinfo_1.3.2 KEGGREST_1.53.6
## [49] IRanges_2.47.5 S4Vectors_0.51.10 bit_4.6.0
## [52] pkgconfig_2.0.3 bslib_0.12.0 pillar_1.11.1
## [55] glue_1.8.1 xfun_0.61 tibble_3.3.1
## [58] tidyselect_1.2.1 sys_3.4.3 knitr_1.52
## [61] htmltools_0.5.9 maketools_1.3.2 compiler_4.6.1