{ "_id": "6a27b03324555f66ed535652", "Package": "HiCDCPlus", "Type": "Package", "Title": "Hi-C Direct Caller Plus", "Version": "1.20.0", "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-release.r-universe.dev", "Date/Publication": "2026-04-28 12:55:01 UTC", "RemoteUrl": "https://github.com/bioc/HiCDCPlus", "RemoteRef": "RELEASE_3_23", "RemoteSha": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "Packaged": { "Date": "2026-06-08 07:22:17 UTC", "User": "root" }, "Author": "Merve Sahin [cre, aut] (ORCID: )", "Maintainer": "Merve Sahin ", "MD5sum": "5f10991b9e17ce91075c31e66168390f", "_user": "bioc-release", "_type": "src", "_file": "HiCDCPlus_1.20.0.tar.gz", "_fileid": "285cc3f32771acb6a753131eb48ed104d8db20345521574b49d9efeee5b717cd", "_filesize": 1241950, "_sha256": "285cc3f32771acb6a753131eb48ed104d8db20345521574b49d9efeee5b717cd", "_created": "2026-06-08T07:22:17.000Z", "_published": "2026-06-09T06:18:27.553Z", "_jobs": [ { "job": 80256728172, "time": 360, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7473917094" }, { "job": 80256728295, "time": 578, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7473981664" }, { "job": 80256728164, "time": 875, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7474067761" }, { "job": 80256728125, "time": 560, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7473976315" }, { "job": 80256727835, "time": 571, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7499616038" }, { "job": 80256728299, "time": 529, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7473966145" }, { "job": 80256727962, "time": 823, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7474051919" }, { "job": 80256727844, "time": 559, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7499923167" }, { "job": 80256728127, "time": 1186, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7474163079" }, { "job": 80256727966, "time": 509, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7473815891" }, { "job": 80256728076, "time": 352, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7473914585" }, { "job": 80256728227, "time": 638, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7473997938" }, { "job": 80256727734, "time": 630, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7499630042" }, { "job": 80256727774, "time": 538, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7499608157" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/HiCDCPlus", "_commit": { "id": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to 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": "noble", "_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": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "hic", "dna3dstructure", "software", "normalization", "zlib", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 335, "source": "https://www.bioconductor.org/packages/stats/bioc/HiCDCPlus" }, "_searchresults": 24, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HiCDCPlus.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "backports", "base64enc", "bbmle", "bdsmatrix", "BH", "Biobase", "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-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "HiCDCPlus.Rmd", "filename": "HiCDCPlus.html", "title": "Analyzing Hi-C and HiChIP data with HiCDCPlus", "author": "Merve Sahin", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Standard workflow", "Overview", "Quickstart", "Finding Significant Interactions from Hi-C/HiChIP", "Finding Differential Interactions", "ICE normalization using HiTC", "Finding TADs using TopDom", "Finding A/B compartment using Juicer", "Creating genomic feature files", "The gi_list instance", "Uniformly binned gi_list instance", "Restriction enzyme binned gi_list instance", "Generating gi_list instance from a bintolen file", "Using custom features with HiCDCPlus", "How to get help for HiCDCPlus", "Session info" ], "created": "2020-10-15 01:04:59", "modified": "2022-05-08 06:51:28", "commits": 9 } ], "_score": 4.380211241711606, "_indexed": false, "_nocasepkg": "hicdcplus", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/HiCDCPlus", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-06-08T07:29:31.000Z", "distro": "noble", "arch": "aarch64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "ab5665d4dcb8a8057fd7e508fcb79583ec52fb1f3e0a406bac82fa23f90d0b4d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-06-08T07:33:11.000Z", "distro": "noble", "arch": "x86_64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "c14a0c9a222fe58c3b7ad8b46b446fa425329bf8b30a57a78c70c4c6342d9020", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-06-08T07:29:11.000Z", "distro": "noble", "arch": "aarch64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "a94057f182c5e031400f246a2324e0f127ecfdbff7fb22bd606efe3b9f296635", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-06-09T05:53:40.000Z", "distro": "noble", "arch": "x86_64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "a82ef84a5927a1b41a6162c8f4e46251095f83a3ff069e449cdd6799b245cbc1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-06-08T07:27:45.000Z", "arch": "aarch64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "1fc473f3961af2226f31e5ea983842b5be58a66d8dca345a958b349eb85c9968", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-06-08T07:30:34.000Z", "arch": "x86_64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "9ad05ce9b7c491578b32a2fc26cca93996941aaf912cd57d4995cc9025c6c9da", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-06-09T06:13:18.000Z", "arch": "aarch64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "75aa8c4e6f7c8d07c17f5723e220214ca905a7885616e507142b74874859e8c6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-06-08T07:35:09.000Z", "arch": "x86_64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "c744b05e2b8b0b48ee9fb49b1905345c9392c97dd76653da460eea786b15d6e9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-06-08T07:29:04.000Z", "arch": "emscripten", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "8fae2121b134324e4c5b707261349420204c5b65d95338c2a0fc2034a23d9657", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-06-08T07:27:58.000Z", "arch": "x86_64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "0d99d86e8552aafeb85966ee16ea6c4caadbb56a99d9b0940b3c25292c86ca5f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-06-09T05:52:07.000Z", "arch": "x86_64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "e2704c67df54e2e70caf91a490159f40e2c407d060022732493449177145d270", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" }, { "r": "4.6.0", "os": "win", "version": "1.20.0", "date": "2026-06-09T05:52:04.000Z", "arch": "x86_64", "commit": "38aa5db3dfaf0e518428df8a2540e62a5fa57db1", "fileid": "7260fa8004fff4be2276b0a2d29baad1d738407f3d8068f279715b757aeba37f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121897510" } ] }