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/4a10f5c903583_8147" 
##                                                          WT 
## "/home/biocbuild/.cache/R/ExperimentHub/4a10f3f19dfcd_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/4a10f7ea77ab3_8168" 
##                                                   LIMA_0030 
## "/home/biocbuild/.cache/R/ExperimentHub/4a10f5919381b_8169" 
##                                                   LIMA_0060 
## "/home/biocbuild/.cache/R/ExperimentHub/4a10f55d53436_8170" 
##                                                   LIMA_0090 
## "/home/biocbuild/.cache/R/ExperimentHub/4a10f4b0c08a7_8171" 
##                                                   LIMA_0120 
## "/home/biocbuild/.cache/R/ExperimentHub/4a10f5370df7f_8172" 
##                                                   LIMA_0240 
## "/home/biocbuild/.cache/R/ExperimentHub/4a10f216efe4c_8173" 
##                                                   LIMA_0360 
##  "/home/biocbuild/.cache/R/ExperimentHub/4a10f35d562c_8174" 
##                                                   LIMA_1440 
## "/home/biocbuild/.cache/R/ExperimentHub/4a10f5311ffd5_8175"

Session information

sessionInfo()

## R Under development (unstable) (2025-10-20 r88955)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 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_1.9.0
## 
## loaded via a namespace (and not attached):
##  [1] rappdirs_0.3.3       sass_0.4.10          generics_0.1.4      
##  [4] BiocVersion_3.22.0   RSQLite_2.4.3        digest_0.6.37       
##  [7] magrittr_2.0.4       evaluate_1.0.5       fastmap_1.2.0       
## [10] blob_1.2.4           AnnotationHub_3.99.6 jsonlite_2.0.0      
## [13] AnnotationDbi_1.71.2 DBI_1.2.3            BiocManager_1.30.26 
## [16] httr_1.4.7           purrr_1.1.0          Biostrings_2.77.2   
## [19] httr2_1.2.1          jquerylib_0.1.4      cli_3.6.5           
## [22] crayon_1.5.3         rlang_1.1.6          XVector_0.49.1      
## [25] dbplyr_2.5.1         Biobase_2.69.1       bit64_4.6.0-1       
## [28] withr_3.0.2          cachem_1.1.0         yaml_2.3.10         
## [31] tools_4.6.0          memoise_2.0.1        dplyr_1.1.4         
## [34] filelock_1.0.3       ExperimentHub_2.99.6 BiocGenerics_0.55.4 
## [37] curl_7.0.0           vctrs_0.6.5          R6_2.6.1            
## [40] png_0.1-8            stats4_4.6.0         BiocFileCache_2.99.6
## [43] lifecycle_1.0.4      Seqinfo_0.99.3       KEGGREST_1.49.2     
## [46] S4Vectors_0.47.4     IRanges_2.43.5       bit_4.6.0           
## [49] pkgconfig_2.0.3      pillar_1.11.1        bslib_0.9.0         
## [52] glue_1.8.0           xfun_0.53            tibble_3.3.0        
## [55] tidyselect_1.2.1     knitr_1.50           htmltools_0.5.8.1   
## [58] rmarkdown_2.30       compiler_4.6.0

marinerData package

Session information