{ "_id": "6a22744ccd65a98ecbd4a22c", "Package": "hicream", "Title": "HIC diffeREntial Analysis Method", "Version": "0.0.4", "Date": "2026-01-30", "Maintainer": "Elise Jorge ", "Authors@R": "c(\nperson(\"Elise\", \"Jorge\", , \"elise.jorge@inrae.fr\", role = c(\"aut\", \"cre\")),\nperson(\"Sylvain\", \"Foissac\", , \"sylvain.foissac@inrae.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-2631-5356\")),\nperson(\"Toby\", \"Hocking\", , \"toby.hocking@r-project.org\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3146-0865\")),\nperson(\"Pierre\", \"Neuvial\", , \"pierre.neuvial@math.univ-toulouse.fr\",\nrole = \"aut\", comment = c(ORCID = \"0000-0003-3584-9998\")),\nperson(\"Nathalie\", \"Vialaneix\", , \"nathalie.vialaneix@inrae.fr\",\nrole = \"aut\", comment = c(ORCID = \"0000-0003-1156-0639\")),\nperson(\"Gilles\", \"Blanchard\", role = \"ctb\"),\nperson(\"Guillermo\", \"Durand\", role= \"ctb\",\ncomment = c(ORCID = \"0000-0003-4056-5631\")),\nperson(\"Nicolas\", \"Enjalbert-Courrech\", role = \"ctb\"),\nperson(\"Etienne\", \"Roquain\", role = \"ctb\")\n)", "Description": "Perform Hi-C data differential analysis based on\npixel-level differential analysis and a post hoc inference\nstrategy to quantify signal in clusters of pixels. Clusters of\npixels are obtained through a connectivity-constrained\ntwo-dimensional hierarchical clustering.", "License": "GPL (>= 3)", "URL": "https://scales.pages-forge.inrae.fr/hicream/,\nhttps://forge.inrae.fr/scales/hicream", "BugReports": "https://forge.inrae.fr/scales/hicream/-/issues", "SystemRequirements": "Python (>= 3.9)", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 06:52:49 UTC", "User": "root" }, "Author": "Elise Jorge [aut, cre], Sylvain Foissac [aut] (ORCID:\n), Toby Hocking [aut]\n(ORCID: ), Pierre\nNeuvial [aut] (ORCID: ),\nNathalie Vialaneix [aut] (ORCID:\n), Gilles Blanchard\n[ctb], Guillermo Durand [ctb] (ORCID:\n), Nicolas\nEnjalbert-Courrech [ctb], Etienne Roquain [ctb]", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev python3 libx11-dev xz-utils zlib1g-dev", "Repository": "https://eoojj.r-universe.dev", "Date/Publication": "2026-01-30 15:50:02 UTC", "RemoteUrl": "https://github.com/cran/hicream", "RemoteRef": "HEAD", "RemoteSha": "b003479e57030d3007e897943556f668cf536fc5", "MD5sum": "d55e8d6b4bb5300e0d1d9041f3182690", "_user": "eoojj", "_type": "src", "_file": "hicream_0.0.4.tar.gz", "_fileid": "ca087795cd5ab095b1d59cd64a5d063fd925cf949061dd4f74287b2772de202b", "_filesize": 424814, "_sha256": "ca087795cd5ab095b1d59cd64a5d063fd925cf949061dd4f74287b2772de202b", "_created": "2026-06-05T06:52:49.000Z", "_published": "2026-06-05T07:01:31.997Z", "_distro": "noble", "_jobs": [ { "job": 79679014467, "time": 383, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7430679211" }, { "job": 79679014468, "time": 418, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7430687085" }, { "job": 79679014399, "time": 357, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7430664997" }, { "job": 79679014406, "time": 428, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7430679317" }, { "job": 79678357166, "time": 325, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7430587495" }, { "job": 79679014385, "time": 189, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7430633405" }, { "job": 79679014423, "time": 322, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7430664650" }, { "job": 79679014436, "time": 335, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7430668049" }, { "job": 79679014431, "time": 352, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7430672121" } ], "_buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/hicream", "_commit": { "id": "b003479e57030d3007e897943556f668cf536fc5", "author": "Elise Jorge ", "committer": "cran-robot ", "message": "version 0.0.4\n", "time": 1769788202 }, "_maintainer": { "name": "Elise Jorge", "email": "elise.jorge@inrae.fr", "login": "eoojj", "description": "", "uuid": 230034486 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "reticulate", "role": "Depends" }, { "package": "adjclust", "role": "Imports" }, { "package": "auk", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "csaw", "role": "Imports" }, { "package": "diffHic", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "InteractionSet", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-47", "n": 1 }, { "week": "2026-03", "n": 1 }, { "week": "2026-05", "n": 1 } ], "_tags": [ { "name": "0.0.1", "date": "2025-07-25" }, { "name": "0.0.2", "date": "2025-11-19" }, { "name": "0.0.3", "date": "2026-01-12" }, { "name": "0.0.4", "date": "2026-01-30" } ], "_stars": 0, "_contributors": [ { "user": "eoojj", "count": 4, "uuid": 230034486 } ], "_userbio": { "uuid": 230034486, "type": "user", "name": "eoojj" }, "_downloads": { "count": 159, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hicream" }, "_pkgdown": "https://scales.pages-forge.inrae.fr/hicream/", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hicream.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "eoojj", "_cranurl": false, "_releases": [ { "version": "0.0.1", "date": "2025-07-25" }, { "version": "0.0.2", "date": "2025-11-19" }, { "version": "0.0.3", "date": "2026-01-12" }, { "version": "0.0.4", "date": "2026-01-30" } ], "_exports": [ "AggloClust2D", "loadData", "performTest", "postHoc" ], "_datasets": [ { "name": "pighic", "title": "Dataset \"pighic\"", "object": "pighic", "file": "pighic.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "AggloClust2D", "title": "Perform Constrained 2D Agglomerative Clustering", "topics": [ "AggloClust2D", "plot.res2D", "print.res2D", "summary.res2D" ] }, { "page": "loadData", "title": "Load and Normalize Hi-C Data", "topics": [ "loadData" ] }, { "page": "performTest", "title": "Perform diffHic Test", "topics": [ "performTest", "plot.resdiff", "print.resdiff", "summary.resdiff" ] }, { "page": "pighic", "title": "Dataset \"pighic\"", "topics": [ "pighic" ] }, { "page": "postHoc", "title": "Perform Post Hoc Inference", "topics": [ "plot.resposthoc", "postHoc", "print.resposthoc", "summary.resposthoc" ] } ], "_readme": "https://github.com/cran/hicream/raw/HEAD/README.md", "_rundeps": [ "abind", "adjclust", "askpass", "assertthat", "auk", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "BSgenome", "capushe", "cigarillo", "cli", "clipr", "codetools", "countrycode", "cpp11", "crayon", "csaw", "curl", "DelayedArray", "dendextend", "diffHic", "dir.expiry", "dplyr", "edgeR", "farver", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "here", "hms", "httr", "InteractionSet", "IRanges", "isoband", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "metapod", "mime", "openssl", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppTOML", "RCurl", "readr", "reshape2", "restfulr", "reticulate", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "rprojroot", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "UCSC.utils", "utf8", "vctrs", "viridis", "viridisLite", "vroom", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "A-Installation.Rmd", "filename": "A-Installation.html", "title": "Installation instructions for hicream", "author": "Elise Jorge, Sylvain Foissac, Pierre Neuvial, and Nathalie Vialaneix", "engine": "knitr::rmarkdown", "headings": [ "AWK", "Python dependencies", "Session information" ], "created": "2025-07-25 15:40:02", "modified": "2025-11-19 17:20:02", "commits": 2 }, { "source": "B-Introduction.Rmd", "filename": "B-Introduction.html", "title": "Introduction to hicream", "author": "Elise Jorge, Sylvain Foissac, Pierre Neuvial, et Nathalie Vialaneix", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "How to load external data?", "pighic dataset", "Perform hicream test", "Use performTest function", "Perform two-dimensional connectivity-constrained clustering", "Perform post hoc inference", "Session Information" ], "created": "2025-07-25 15:40:02", "modified": "2025-11-19 17:20:02", "commits": 2 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "hicream", "_universes": [ "eoojj" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.4", "date": "2026-06-05T06:56:13.000Z", "distro": "noble", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "732448f4e58866f56de161304e06e8be8d008b0911bbea9b13b4e67fe04d123f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" }, { "r": "4.6.0", "os": "linux", "version": "0.0.4", "date": "2026-06-05T06:56:37.000Z", "distro": "noble", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "477c0321288c456e9044d62f1caee0a97a0be78fee310a7b1acf32644c589728", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" }, { "r": "4.5.3", "os": "mac", "version": "0.0.4", "date": "2026-06-05T06:56:09.000Z", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "3c318fe17b6789f4070b57016c8a1d8b20ab041f549ff6d0fbba960d9f974121", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" }, { "r": "4.6.0", "os": "mac", "version": "0.0.4", "date": "2026-06-05T06:55:58.000Z", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "0c61b3fd607dddf5d468016c0f562b970f5e41206b9ad5c1ea9e17edcb29290a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.4", "date": "2026-06-05T06:56:41.000Z", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "9dd6c6ae3c186cf8bc60b1a9e8335b0791fb776f8d08b936e71044d8e8186b40", "status": "success", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" }, { "r": "4.7.0", "os": "win", "version": "0.0.4", "date": "2026-06-05T06:55:09.000Z", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "6bcb975a51d1493e8e54d310b6fce035b7a3aed2170e5e39a9941fe301789241", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" }, { "r": "4.5.3", "os": "win", "version": "0.0.4", "date": "2026-06-05T06:55:13.000Z", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "1c59ea849ba211e3ad15ada11b7ff22969df20c0f84f161732e2f57b211896cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" }, { "r": "4.6.0", "os": "win", "version": "0.0.4", "date": "2026-06-05T06:55:27.000Z", "commit": "b003479e57030d3007e897943556f668cf536fc5", "fileid": "439856bab3ea80852cb5a325fd93504a99d52f9e0c358357ef875159cfc3a843", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eoojj/actions/runs/27000072798" } ] }