{ "_id": "6a4940ce18cdde069385dd00", "Package": "bnbc", "Version": "1.35.0", "Title": "Bandwise normalization and batch correction of Hi-C data", "Description": "Tools to normalize (several) Hi-C data from replicates.", "Authors@R": "c(\nperson(\"Kipper\", \"Fletez-Brant\", role = c(\"cre\", \"aut\"), email = \"cafletezbrant@gmail.com\"),\nperson(c(\"Kasper\", \"Daniel\"), \"Hansen\", role = \"aut\"))", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "URL": "https://github.com/hansenlab/bnbc", "BugReports": "https://github.com/hansenlab/bnbc/issues", "biocViews": "HiC, Preprocessing, Normalization, Software", "Config/pak/sysreqs": "cmake libfftw3-dev make libjpeg-dev libpng-dev\nlibtiff-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:39 UTC", "RemoteUrl": "https://github.com/bioc/bnbc", "RemoteRef": "HEAD", "RemoteSha": "3d959e0ddf42e996e4ef841ccad70740de902b89", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-04 06:47:49 UTC", "User": "root" }, "Author": "Kipper Fletez-Brant [cre, aut],\nKasper Daniel Hansen [aut]", "Maintainer": "Kipper Fletez-Brant ", "_user": "bioc", "_type": "src", "_file": "bnbc_1.35.0.tar.gz", "_fileid": "https://r2.ropensci.org/7a5fa6a1e05a588c22cef512257908753d3227d853c964948869596db07df59e", "_filesize": 4210728, "_sha256": "7a5fa6a1e05a588c22cef512257908753d3227d853c964948869596db07df59e", "_expires": "2026-10-12T17:20:12.000Z", "_created": "2026-07-04T06:47:49.000Z", "_published": "2026-07-04T17:20:14.373Z", "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254", "_status": "success", "_upstream": "https://github.com/bioc/bnbc", "_commit": { "id": "3d959e0ddf42e996e4ef841ccad70740de902b89", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380399 }, "_maintainer": { "name": "Kipper Fletez-Brant", "email": "cafletezbrant@gmail.com", "login": "cafletezbrant", "description": "Sr Scientist @ Genentech, previously Sr Scientist @ 23andMe.", "uuid": 2319608 }, "_distro": "resolute", "_jobs": [ { "job": 85151659674, "time": 272, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8079314923" }, { "job": 85151659867, "time": 361, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8079324982" }, { "job": 85151659671, "time": 478, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8079337424" }, { "job": 85151659627, "time": 362, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8079324989" }, { "job": 85151659864, "time": 433, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8079332521" }, { "job": 85151659701, "time": 286, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8079746195" }, { "job": 85151659870, "time": 752, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8079374772" }, { "job": 85151659749, "time": 362, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8079755682" }, { "job": 85151659587, "time": 669, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8079362905" }, { "job": 85151659570, "time": 354, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8079283227" }, { "job": 85151659684, "time": 243, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8079311748" }, { "job": 85151659799, "time": 610, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8079354590" }, { "job": 85151659628, "time": 547, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8079346249" }, { "job": 85151659653, "time": 665, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8079361641" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.12", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "rhdf5", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "preprocessCore", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "EBImage", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23" } ], "_topics": [ "hic", "preprocessing", "normalization", "software", "cpp" ], "_stars": 2, "_contributors": [ { "user": "cafletezbrant", "count": 89, "uuid": 2319608 }, { "user": "kasperdanielhansen", "count": 44, "uuid": 4956575 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "hpages", "count": 3, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 1, "_devurl": "https://github.com/hansenlab/bnbc", "_searchresults": 15, "_rbuild": "4.6.1", "_assets": [ "extra/bnbc.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/hansenlab/bnbc", "_realowner": "bioc", "_cranurl": false, "_exports": [ "band", "band<-", "bnbc", "boxSmoother", "cg2bedgraph2", "cgApply", "cgBandApply", "colData", "colData<-", "ContactGroup", "contacts", "contacts<-", "distanceIdx", "dropGroupZeros", "gaussSmoother", "getBandIdx", "getBandMatrix", "getChrCGFromCools", "getChrIdx", "getGroupZeros", "librarySize", "logCPM", "rowData", "rowData<-", "show" ], "_datasets": [ { "name": "cgEx", "title": "Sample chr22 Data", "object": "cgEx", "file": "cgEx.rda", "class": [ "ContactGroup" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "bnbc-package", "title": "Bandwise normalization and batch correction of Hi-C data", "topics": [ "bnbc-package" ] }, { "page": "band", "title": "Get Band", "topics": [ "band", "band<-" ] }, { "page": "bnbc", "title": "Normalize Contact Matrices with BNBC", "topics": [ "bnbc" ] }, { "page": "apply_functions", "title": "Apply-type methods", "topics": [ "cgApply", "cgBandApply" ] }, { "page": "cgEx", "title": "Sample chr22 Data", "topics": [ "cgEx" ] }, { "page": "ContactGroup-class", "title": "Class '\"ContactGroup\"'", "topics": [ "colData,ContactGroup-method", "colData<-,ContactGroup,DataFrame-method", "ContactGroup", "ContactGroup-class", "contacts", "contacts<-", "dim,ContactGroup-method", "distanceIdx", "librarySize", "logCPM", "rowData,ContactGroup-method", "rowData<-,ContactGroup-method", "show,ContactGroup-method", "[,ContactGroup,ANY,ANY,ANY-method" ] }, { "page": "cooler_methods", "title": "Methods for manipulating cooler files", "topics": [ "cg2bedgraph2", "getChrCGFromCools", "getChrIdx", "getGenomeIdx" ] }, { "page": "getBandIdx", "title": "Get Band Indices", "topics": [ "getBandIdx" ] }, { "page": "getBandMatrix", "title": "Get Band Matrix", "topics": [ "getBandMatrix" ] }, { "page": "groupZeros", "title": "Group Zero Operations", "topics": [ "dropGroupZeros", "getGroupZeros" ] }, { "page": "smoothing", "title": "Smoothing Operations", "topics": [ "boxSmoother", "gaussSmoother" ] } ], "_readme": "https://github.com/bioc/bnbc/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocGenerics", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "digest", "dir.expiry", "EBImage", "edgeR", "evaluate", "fastmap", "fftwtools", "filelock", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "genefilter", "generics", "GenomicRanges", "glue", "highr", "htmltools", "htmlwidgets", "httr", "IRanges", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "openssl", "pkgconfig", "png", "preprocessCore", "R6", "rappdirs", "Rcpp", "RCurl", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "rmarkdown", "RSQLite", "S4Arrays", "S4Vectors", "sass", "Seqinfo", "snow", "SparseArray", "statmod", "SummarizedExperiment", "survival", "sva", "sys", "tiff", "tinytex", "vctrs", "xfun", "XML", "xtable", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "bnbc.Rmd", "filename": "bnbc.html", "title": "The bnbc User's Guide", "author": "Kipper Fletez-Brant, Kasper Daniel Hansen", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Citing bnbc", "Terminology", "Dependencies", "The ContactGroup class from bnbc", "Alternatives", "Getting your data into bnbc", "Getting your data out of *.cooler files", "Working with bnbc contact matrices", "Per-Sample Adjustments", "Cross Sample Normalization", "sessionInfo()", "References" ], "created": "2017-08-30 15:10:47", "modified": "2026-04-26 20:43:16", "commits": 24 } ], "_score": 5.477121254719663, "_indexed": true, "_nocasepkg": "bnbc", "_universes": [ "bioc", "cafletezbrant", "hansenlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-07-04T06:52:02.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/7e185bc34cff6ab28c62eef743130416690b799cb1628b4526d4db07bd8fbaae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-07-04T06:53:02.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/4d99fe412a1f30d172e8c6096208322de77f1289018527c388d7ba8d5acbfb27", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.6.1", "os": "linux", "version": "1.35.0", "date": "2026-07-04T06:52:03.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/65d6be395fe4ba76e77a3128957e94c915a2731bd84e2eb8944877aa62f0520b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.6.1", "os": "linux", "version": "1.35.0", "date": "2026-07-04T06:52:31.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/c4479dfc9f44557eeb24884cc4aeab51dc5aecf6cdfd172dd8ff45cddf720425", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-07-04T07:44:48.000Z", "arch": "aarch64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/1832899ccd2c14b00597c0827a39642146b65c6c70b55ee677132549f253d020", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-07-04T06:54:37.000Z", "arch": "x86_64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/d7db38f67181e4ef4290f1bf4e6174c83cdef56196c9e337e1ef7253a56cf6ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.6.1", "os": "mac", "version": "1.35.0", "date": "2026-07-04T07:45:13.000Z", "arch": "aarch64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/c2052867037b110fd7aee1ff58eac8d484074fd2af5c3eb207f1c4fa3f1d76b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.6.1", "os": "mac", "version": "1.35.0", "date": "2026-07-04T06:54:48.000Z", "arch": "x86_64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/d7fd1620473b7cbd2b703a4b322708139057e6984b6d5552381997a08ae213f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-07-04T06:52:33.000Z", "arch": "emscripten", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/9001374323e33de751d64008a135bb46900267381f1e5b7790ba24383b22feac", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-07-04T06:54:37.000Z", "arch": "x86_64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/06f7586f6623a061774a885100dfff3d4a766abe1bafb6db231965104a9831c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-07-04T06:54:05.000Z", "arch": "x86_64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/56700a776656aa3269a63a612c0768f6ae68a71530f5582e7521b8c50e141fbe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" }, { "r": "4.6.1", "os": "win", "version": "1.35.0", "date": "2026-07-04T06:55:12.000Z", "arch": "x86_64", "commit": "3d959e0ddf42e996e4ef841ccad70740de902b89", "fileid": "https://r2.ropensci.org/e21110cd1b0e30c8aaccc393ad9120d2a379bfe14df8574ae545193aafad20bf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28698062254" } ] }