{ "_id": "6ad34f2ade48616761a36b85", "Package": "HiCDCPlus", "Type": "Package", "Title": "Hi-C Direct Caller Plus", "Version": "1.21.0", "Description": "Systematic 3D interaction calls and differential analysis\nfor Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller\nplus) package enables principled statistical analysis of Hi-C\nand HiChIP data sets – including calling significant\ninteractions within a single experiment and performing\ndifferential analysis between conditions given replicate\nexperiments – to facilitate global integrative studies. HiC-DC+\nestimates significant interactions in a Hi-C or HiChIP\nexperiment directly from the raw contact matrix for each\nchromosome up to a specified genomic distance, binned by\nuniform genomic intervals or restriction enzyme fragments, by\ntraining a background model to account for random polymer\nligation and systematic sources of read count variation.", "Authors@R": "person(\"Merve\", \"Sahin\", email=\"merve.sahn@gmail.com\", role=c(\"cre\",\"aut\"), comment=c(ORCID = \"0000-0003-3858-8332\"))", "License": "GPL-3", "Encoding": "UTF-8", "biocViews": "HiC, DNA3DStructure, Software, Normalization", "RoxygenNote": "7.1.1", "SystemRequirements": "JRE 8+", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:01 UTC", "RemoteUrl": "https://github.com/bioc/HiCDCPlus", "RemoteRef": "HEAD", "RemoteSha": "be86a097c5b832816450744455b97f2f03e0a9aa", "Packaged": { "Date": "2026-10-17 10:18:25 UTC", "User": "root" }, "Author": "Merve Sahin [cre, aut] (ORCID: )", "Maintainer": "Merve Sahin ", "_user": "bioc", "_type": "src", "_file": "HiCDCPlus_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/54bd5161b9cdfb43cb73771adecb203f1512a415e4350945faeab3fcf4f97af4", "_filesize": 1221188, "_sha256": "54bd5161b9cdfb43cb73771adecb203f1512a415e4350945faeab3fcf4f97af4", "_expires": "2027-01-25T10:34:16.000Z", "_created": "2026-10-17T10:18:25.000Z", "_published": "2026-10-17T10:34:18.812Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529", "_status": "failure", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 2, "note": 11 }, "_upstream": "https://github.com/bioc/HiCDCPlus", "_commit": { "id": "be86a097c5b832816450744455b97f2f03e0a9aa", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380901 }, "_maintainer": { "name": "Merve Sahin", "email": "merve.sahn@gmail.com", "login": "mervesa", "description": "", "uuid": 3522471, "orcid": "0000-0003-3858-8332" }, "_distro": "resolute", "_jobs": [ { "job": 117372542441, "time": 292, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "12098391072" }, { "job": 117372542444, "time": 402, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "12097777332" }, { "job": 117372542433, "time": 500, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "12097738908" }, { "job": 117372542575, "time": 366, "config": "linux-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "12098421044" }, { "job": 117372542476, "time": 530, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "12097404295" }, { "job": 117372542523, "time": 357, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "12098710103" }, { "job": 117372542549, "time": 575, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "12098097654" }, { "job": 117372542494, "time": 477, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12098620452" }, { "job": 117372542474, "time": 885, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12098715795" }, { "job": 117371043766, "time": 492, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "12097249080" }, { "job": 117372542512, "time": 323, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12098137070" }, { "job": 117372542524, "time": 472, "config": "windows-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "12098700114" }, { "job": 117372542471, "time": 355, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "12098245849" }, { "job": 117372542517, "time": 390, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "12098326442" }, { "job": 117372542547, "time": 499, "config": "windows-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "12097099864" }, { "job": 117372542502, "time": 446, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12098356471" } ], "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "InteractionSet", "role": "Imports" }, { "package": "GenomicInteractions", "role": "Imports" }, { "package": "bbmle", "role": "Imports" }, { "package": "pscl", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "BSgenome.Mmusculus.UCSC.mm9", "role": "Suggests" }, { "package": "BSgenome.Mmusculus.UCSC.mm10", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "HiTC", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "rappdirs", "role": "Suggests" }, { "package": "parallel", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "hic", "dna3dstructure", "software", "normalization", "zlib", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 477, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 580, "source": "https://www.bioconductor.org/packages/stats/bioc/HiCDCPlus" }, "_searchresults": 31, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HiCDCPlus.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "add_1D_features", "add_2D_features", "add_hic_counts", "add_hicpro_allvalidpairs_counts", "add_hicpro_matrix_counts", "construct_features", "construct_features_chr", "construct_features_parallel", "expand_1D_features", "extract_hic_eigenvectors", "generate_binned_gi_list", "generate_bintolen_gi_list", "generate_df_gi_list", "get_chr_sizes", "get_chrs", "get_enzyme_cutsites", "gi_list_binsize_detect", "gi_list_Dthreshold.detect", "gi_list_read", "gi_list_topdom", "gi_list_validate", "gi_list_write", "gi_list2HTClist", "hic2icenorm_gi_list", "hicdc2hic", "hicdcdiff", "HiCDCPlus", "HiCDCPlus_chr", "HiCDCPlus_parallel", "HTClist2gi_list", "straw", "straw_dump" ], "_help": [ { "page": "add_1D_features", "title": "add_1D_features", "topics": [ "add_1D_features" ] }, { "page": "add_2D_features", "title": "add_2D_features", "topics": [ "add_2D_features" ] }, { "page": "add_hic_counts", "title": "add_hic_counts", "topics": [ "add_hic_counts" ] }, { "page": "add_hicpro_allvalidpairs_counts", "title": "add_hicpro_allvalidpairs_counts", "topics": [ "add_hicpro_allvalidpairs_counts" ] }, { "page": "add_hicpro_matrix_counts", "title": "add_hicpro_matrix.counts", "topics": [ "add_hicpro_matrix_counts" ] }, { "page": "construct_features", "title": "construct_features", "topics": [ "construct_features" ] }, { "page": "construct_features_chr", "title": "construct_features_chr", "topics": [ "construct_features_chr" ] }, { "page": "construct_features_parallel", "title": "construct_features_parallel", "topics": [ "construct_features_parallel" ] }, { "page": "expand_1D_features", "title": "expand_1D_features", "topics": [ "expand_1D_features" ] }, { "page": "extract_hic_eigenvectors", "title": "extract_hic_eigenvectors", "topics": [ "extract_hic_eigenvectors" ] }, { "page": "generate_binned_gi_list", "title": "generate_binned_gi_list", "topics": [ "generate_binned_gi_list" ] }, { "page": "generate_bintolen_gi_list", "title": "generate_bintolen_gi_list", "topics": [ "generate_bintolen_gi_list" ] }, { "page": "generate_df_gi_list", "title": "generate_df_gi_list", "topics": [ "generate_df_gi_list" ] }, { "page": "get_chr_sizes", "title": "get_chr_sizes", "topics": [ "get_chr_sizes" ] }, { "page": "get_chrs", "title": "get_chrs", "topics": [ "get_chrs" ] }, { "page": "get_enzyme_cutsites", "title": "get_enzyme_cutsites", "topics": [ "get_enzyme_cutsites" ] }, { "page": "gi_list_binsize_detect", "title": "gi_list_binsize_detect", "topics": [ "gi_list_binsize_detect" ] }, { "page": "gi_list_Dthreshold.detect", "title": "gi_list_Dthreshold_detect", "topics": [ "gi_list_Dthreshold.detect" ] }, { "page": "gi_list_read", "title": "gi_list_read", "topics": [ "gi_list_read" ] }, { "page": "gi_list_topdom", "title": "gi_list_topdom", "topics": [ "gi_list_topdom" ] }, { "page": "gi_list_validate", "title": "gi_list_validate", "topics": [ "gi_list_validate" ] }, { "page": "gi_list_write", "title": "gi_list_write", "topics": [ "gi_list_write" ] }, { "page": "gi_list2HTClist", "title": "gi_list2HTClist", "topics": [ "gi_list2HTClist" ] }, { "page": "hic2icenorm_gi_list", "title": "hic2icenorm_gi_list", "topics": [ "hic2icenorm_gi_list" ] }, { "page": "hicdc2hic", "title": "hicdc2hic", "topics": [ "hicdc2hic" ] }, { "page": "hicdcdiff", "title": "hicdcdiff", "topics": [ "hicdcdiff" ] }, { "page": "HiCDCPlus", "title": "HiCDCPlus", "topics": [ "HiCDCPlus" ] }, { "page": "HiCDCPlus_chr", "title": "HiCDCPlus_chr", "topics": [ "HiCDCPlus_chr" ] }, { "page": "HiCDCPlus_parallel", "title": "HiCDCPlus_parallel", "topics": [ "HiCDCPlus_parallel" ] }, { "page": "HTClist2gi_list", "title": "HTClist2gi_list", "topics": [ "HTClist2gi_list" ] }, { "page": "straw", "title": "straw", "topics": [ "straw" ] }, { "page": "straw_dump", "title": "straw_dump", "topics": [ "straw_dump" ] } ], "_readme": "https://github.com/bioc/HiCDCPlus/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "backports", "base64enc", "bbmle", "bdsmatrix", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "dichromat", "digest", "dplyr", "ensembldb", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicInteractions", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "Gviz", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "InteractionSet", "interp", "IRanges", "isoband", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "latticeExtra", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "mvtnorm", "nnet", "numDeriv", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ProtGenerics", "pscl", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg+really1.3.1-1ubuntu3.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 3.4913616938342726, "_indexed": true, "_nocasepkg": "hicdcplus", "_universes": [ "bioc", "mervesa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-10-17T10:23:54.000Z", "distro": "resolute", "arch": "aarch64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/85ec8730ea648109f82a293eb48d6b558b466e521f3b3de121012406dc037e47", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-10-17T10:24:58.000Z", "distro": "resolute", "arch": "x86_64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/13a1614923a191dd885b0f78ca6dfed9d545e7d7cdd767d814eeccf63877f09d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.6.1", "os": "linux", "version": "1.21.0", "date": "2026-10-17T10:23:30.000Z", "distro": "resolute", "arch": "aarch64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/91832e15aae69a95d2d179ee6c302571718676f381f1dd597aaa977ebf8da6aa", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.6.1", "os": "linux", "version": "1.21.0", "date": "2026-10-17T10:25:47.000Z", "distro": "resolute", "arch": "x86_64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/af756fcd5549a68d29c71b5022847a1cd5dcbd8808a8fc3719ddd0e7c35b0eba", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-10-17T10:23:48.000Z", "arch": "aarch64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/bcfd9ff782d7f49873ad9d4a2933dde8c9980e34dca132d8b50abb5783752c13", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-10-17T10:25:42.000Z", "arch": "x86_64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/d98c11d26736c3c565a3fac57bbd633c51700f77a18e6c5ed9034817315c62a5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.6.1", "os": "mac", "version": "1.21.0", "date": "2026-10-17T10:23:26.000Z", "arch": "aarch64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/28d8a3cc9185b578a82561a91b29ca9ec933573d7ad5ff7c761c5a7514b05993", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.6.1", "os": "mac", "version": "1.21.0", "date": "2026-10-17T10:27:41.000Z", "arch": "x86_64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/91faabeadd3212ecc6488ef8ed6c85e59d9014f15ef0c74837be94b3270c2b54", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-10-17T10:24:23.000Z", "arch": "emscripten", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/1819cac5e1b8a6bc29c5a8340897968a771e3d7327b98e5b117d303ad6707036", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-10-17T10:24:23.000Z", "arch": "aarch64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/824ecaec7377489a97278ffdb92d425b33e44ad4c436bc6d8c28ea2cea8f1f53", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-10-17T10:21:58.000Z", "arch": "x86_64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/d053d04130d7f65dc9d0607d0c81c4eeedeba46a6124cfe82119c5a7b559e21f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-10-17T10:22:35.000Z", "arch": "x86_64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/741e5d2f9721a848f4bb8c0e62822717c2c0c05f99023230c08e6bbb81ee8fb6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.6.1", "os": "win", "version": "1.21.0", "date": "2026-10-17T10:25:07.000Z", "arch": "aarch64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/a59e49085449c9b14615b68b5f2a6f52e147d7451d882059236ac8931e831249", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" }, { "r": "4.6.1", "os": "win", "version": "1.21.0", "date": "2026-10-17T10:22:26.000Z", "arch": "x86_64", "commit": "be86a097c5b832816450744455b97f2f03e0a9aa", "fileid": "https://r2.ropensci.org/a59ace6c0cc37014f3389f62655c1c9a826ff9c9df945b73fae14092ed38269c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023897529" } ] }