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
## 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
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
## 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

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
## 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
## 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"

Session information

sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-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_1.2.0
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.42.0               xfun_0.40                    
##  [3] bslib_0.5.1                   Biobase_2.62.0               
##  [5] bitops_1.0-7                  vctrs_0.6.4                  
##  [7] tools_4.3.1                   generics_0.1.3               
##  [9] stats4_4.3.1                  curl_5.1.0                   
## [11] tibble_3.2.1                  fansi_1.0.5                  
## [13] AnnotationDbi_1.64.0          RSQLite_2.3.1                
## [15] blob_1.2.4                    pkgconfig_2.0.3              
## [17] dbplyr_2.3.4                  S4Vectors_0.40.0             
## [19] GenomeInfoDbData_1.2.11       lifecycle_1.0.3              
## [21] compiler_4.3.1                Biostrings_2.70.1            
## [23] GenomeInfoDb_1.38.0           httpuv_1.6.12                
## [25] htmltools_0.5.6.1             sass_0.4.7                   
## [27] RCurl_1.98-1.12               yaml_2.3.7                   
## [29] interactiveDisplayBase_1.40.0 pillar_1.9.0                 
## [31] later_1.3.1                   crayon_1.5.2                 
## [33] jquerylib_0.1.4               ellipsis_0.3.2               
## [35] cachem_1.0.8                  mime_0.12                    
## [37] ExperimentHub_2.10.0          AnnotationHub_3.10.0         
## [39] tidyselect_1.2.0              digest_0.6.33                
## [41] purrr_1.0.2                   dplyr_1.1.3                  
## [43] BiocVersion_3.18.0            fastmap_1.1.1                
## [45] cli_3.6.1                     magrittr_2.0.3               
## [47] utf8_1.2.4                    withr_2.5.1                  
## [49] filelock_1.0.2                promises_1.2.1               
## [51] rappdirs_0.3.3                bit64_4.0.5                  
## [53] rmarkdown_2.25                XVector_0.42.0               
## [55] httr_1.4.7                    bit_4.0.5                    
## [57] png_0.1-8                     memoise_2.0.1                
## [59] shiny_1.7.5.1                 evaluate_0.22                
## [61] knitr_1.44                    IRanges_2.36.0               
## [63] BiocFileCache_2.10.0          rlang_1.1.1                  
## [65] Rcpp_1.0.11                   xtable_1.8-4                 
## [67] glue_1.6.2                    DBI_1.1.3                    
## [69] BiocManager_1.30.22           BiocGenerics_0.48.0          
## [71] jsonlite_1.8.7                R6_2.5.1                     
## [73] zlibbioc_1.48.0