{ "_id": "6a1be1351d7bb097a0a18638", "Package": "Site2Target", "Type": "Package", "Title": "An R package to associate peaks and target genes", "Version": "1.4.0", "Authors@R": "person(\"Peyman Zarrineh\", email=\"peyman.zarrineh@manchester.ac.uk\", role=c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-4820-4101\"))", "Description": "Statistics implemented for both peak-wise and gene-wise\nassociations. In peak-wise associations, the p-value of the\ntarget genes of a given set of peaks are calculated. Negative\nbinomial or Poisson distributions can be used for modeling the\nunweighted peaks targets and log-nromal can be used to model\nthe weighted peaks. In gene-wise associations a table\nconsisting of a set of genes, mapped to specific peaks, is\ngenerated using the given rules.", "BugReports": "https://github.com/fls-bioinformatics-core/Site2Target/issues", "License": "GPL-2", "Encoding": "UTF-8", "biocViews": "Annotation, ChIPSeq, Software, Epigenetics, GeneExpression,\nGeneTarget", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:04:44 UTC", "RemoteUrl": "https://github.com/bioc/Site2Target", "RemoteRef": "RELEASE_3_23", "RemoteSha": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:37:23 UTC", "User": "root" }, "Author": "Peyman Zarrineh [cre, aut] (ORCID:\n)", "Maintainer": "Peyman Zarrineh ", "MD5sum": "2e241a700a8077c9178ea8f901414a82", "_user": "bioc-release", "_type": "src", "_file": "Site2Target_1.4.0.tar.gz", "_fileid": "2032f920b752239cd3428c01e370e7977702e53d1cac11ced1b61c6bb8055fec", "_filesize": 361388, "_sha256": "2032f920b752239cd3428c01e370e7977702e53d1cac11ced1b61c6bb8055fec", "_created": "2026-05-31T06:37:23.000Z", "_published": "2026-05-31T07:20:21.972Z", "_jobs": [ { "job": 78706056842, "time": 145, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7314500482" }, { "job": 78706056844, "time": 215, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7314508189" }, { "job": 78706056839, "time": 182, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7314504832" }, { "job": 78706056845, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7314750066" }, { "job": 78706056843, "time": 121, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7314733215" }, { "job": 78705879057, "time": 184, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314483711" }, { "job": 78706056848, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314496449" }, { "job": 78706056851, "time": 117, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7314497402" }, { "job": 78706056850, "time": 102, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7314495562" }, { "job": 78706056847, "time": 81, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7314493155" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Site2Target", "_commit": { "id": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "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": 1777381484 }, "_maintainer": { "name": "Peyman Zarrineh", "email": "peyman.zarrineh@manchester.ac.uk", "login": "peymanzarrineh", "description": "", "uuid": 13946474, "orcid": "0000-0003-4820-4101" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23" } ], "_topics": [ "annotation", "chipseq", "software", "epigenetics", "geneexpression", "genetarget" ], "_stars": 0, "_contributors": [ { "user": "peymanzarrineh", "count": 17, "uuid": 13946474 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 220, "source": "https://www.bioconductor.org/packages/stats/bioc/Site2Target" }, "_devurl": "https://github.com/fls-bioinformatics-core/site2target", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "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", "extra/Site2Target.html", "manual.pdf" ], "_homeurl": "https://github.com/fls-bioinformatics-core/site2target", "_realowner": "bioc", "_cranurl": false, "_exports": [ "addColumn2geneWiseAssociation", "addRelation2geneWiseAssociation", "extendSitesInGivenRegions", "genewiseAssociation", "getCenterOfPeaks", "getTargetGenesNumber", "getTargetGenesPvals", "getTargetGenesPvalsWithDNAInteractions", "getTargetGenesPvalsWithIntensities", "getTargetGenesPvalsWithIntensitiesAndDNAInteractions", "granges2String", "removeReserveCharacter", "string2Granges", "Table2Granges" ], "_help": [ { "page": "addColumn2geneWiseAssociation", "title": "Add column to gene-wise association", "topics": [ "addColumn2geneWiseAssociation" ] }, { "page": "addRelation2geneWiseAssociation", "title": "Add a relation column to gene-peak interaction table", "topics": [ "addRelation2geneWiseAssociation" ] }, { "page": "data", "title": "MEIS cardiomyocytes datasets used in the package", "topics": [ "data" ] }, { "page": "extendSitesInGivenRegions", "title": "Extend sites given regions boundaries", "topics": [ "extendSitesInGivenRegions" ] }, { "page": "genewiseAssociation", "title": "Generate genewise association between genes and peaks", "topics": [ "genewiseAssociation" ] }, { "page": "getCenterOfPeaks", "title": "Return center of the given granges files", "topics": [ "getCenterOfPeaks" ] }, { "page": "getNameFromCoordinates", "title": "Get names of genes or peaks related to a query coordinates", "topics": [ "getNameFromCoordinates" ] }, { "page": "getTargetGenesNumber", "title": "generate number of sites per gene given distances", "topics": [ "getTargetGenesNumber" ] }, { "page": "getTargetGenesPvals", "title": "Fit Negative binomial distribution to target genes", "topics": [ "getTargetGenesPvals" ] }, { "page": "getTargetGenesPvalsWithDNAInteractions", "title": "Fit Negative binomial distribution to target genes", "topics": [ "getTargetGenesPvalsWithDNAInteractions" ] }, { "page": "getTargetGenesPvalsWithIntensities", "title": "Fit log-normal distribution to target genes", "topics": [ "getTargetGenesPvalsWithIntensities" ] }, { "page": "getTargetGenesPvalsWithIntensitiesAndDNAInteractions", "title": "Fit log-normal distribution to target genes", "topics": [ "getTargetGenesPvalsWithIntensitiesAndDNAInteractions" ] }, { "page": "granges2String", "title": "Convert granges to strings of coordinates", "topics": [ "granges2String" ] }, { "page": "removeReserveCharacter", "title": "Remove reserved characters from a string", "topics": [ "removeReserveCharacter" ] }, { "page": "site2GeneDistance", "title": "Return the distance between paired peaks and genes", "topics": [ "site2GeneDistance" ] }, { "page": "Site2Target", "title": "Associate peaks and target genes", "topics": [ "Site2Target" ] }, { "page": "string2Granges", "title": "Convert strings to granges of coordinates", "topics": [ "string2Granges" ] }, { "page": "Table2Granges", "title": "Take Genomic Ranges from a table file", "topics": [ "Table2Granges" ] } ], "_readme": "https://github.com/bioc/Site2Target/raw/RELEASE_3_23/README.md", "_rundeps": [ "askpass", "BiocGenerics", "curl", "generics", "GenomeInfoDb", "GenomicRanges", "httr", "IRanges", "jsonlite", "MASS", "mime", "openssl", "R6", "S4Vectors", "Seqinfo", "sys", "UCSC.utils" ], "_vignettes": [ { "source": "Site2Target.Rmd", "filename": "Site2Target.html", "title": "'Site2Target': an R package to associate peaks and target genes", "author": "Peyman Zarrineh", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Introduction", "Motivation for Submitting to Bioconductor", "Overview", "Major functions of Site2Target", "Peakwise-association", "Genewise-association", "Session Info", "References" ], "created": "2024-10-12 18:02:49", "modified": "2025-01-15 18:29:26", "commits": 3 } ], "_score": 4, "_indexed": false, "_nocasepkg": "site2target", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/Site2Target", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-05-31T06:40:27.000Z", "distro": "noble", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "f3de0c665f0344372f030c89d263c2375eb196880dc259789fca9c3492a515c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" }, { "r": "4.6.0", "os": "linux", "version": "1.4.0", "date": "2026-05-31T06:39:57.000Z", "distro": "noble", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "fdb434298185bd71505531b617364b287f74ce3c5e4c84af0c5344a2f0f127c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" }, { "r": "4.5.3", "os": "mac", "version": "1.4.0", "date": "2026-05-31T07:19:31.000Z", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "24d836ce8aa218f2a80642c8f4172e52ace558f81758a5820f08e4a5fde9ceb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" }, { "r": "4.6.0", "os": "mac", "version": "1.4.0", "date": "2026-05-31T07:17:04.000Z", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "5c4dfb43854b2b4383264998f40a0d05c24288c7c5b217f5b2e7ac7176c74153", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0", "date": "2026-05-31T06:39:28.000Z", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "e88d70dae84ad8f66c84c6adb23587dd5758e11217eb40f9074ab54d386d2bea", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-05-31T06:38:49.000Z", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "a5311c082413bc2cd76925857ce7d2f8bb7f0f837620dbf86323d6b97ffe03b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" }, { "r": "4.5.3", "os": "win", "version": "1.4.0", "date": "2026-05-31T06:38:32.000Z", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "3d532d0de65fe5a2bfde0038a9b055b082ddc1d346dc580041bc9461dd68cf8b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" }, { "r": "4.6.0", "os": "win", "version": "1.4.0", "date": "2026-05-31T06:38:19.000Z", "commit": "ce9001280a619e0fc8dacf0ca1bd037c984e5d08", "fileid": "016b0d87ad7f053a4fc16346aa74d85fc5ccb9ee37ed8b014f11a9796f33825a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705488832" } ] }