{ "_id": "6ae5d316327abcdf8686a219", "Package": "SeqGate", "Type": "Package", "Title": "Filtering of Lowly Expressed Features", "Version": "1.23.0", "Date": "2021-01-22", "Authors@R": "c(\nperson(\"Christelle\", \"Reynès\", email =\"christelle.reynes@igf.cnrs.fr\", role = c(\"aut\")),\nperson(\"Stéphanie\", \"Rialle\", email = \"stephanie.rialle@mgx.cnrs.fr\", role = c(\"aut\",\"cre\")))", "Description": "Filtering of lowly expressed features (e.g. genes) is a\ncommon step before performing statistical analysis, but an\narbitrary threshold is generally chosen. SeqGate implements a\nmethod that rationalize this step by the analysis of the\ndistibution of counts in replicate samples. The gate is the\nthreshold above which sequenced features can be considered as\nconfidently quantified.", "Encoding": "UTF-8", "License": "GPL (>= 2.0)", "LazyData": "no", "biocViews": "DifferentialExpression, GeneExpression, Transcriptomics,\nSequencing, RNASeq", "BugReports": "https://github.com/srialle/SeqGate/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:47 UTC", "RemoteUrl": "https://github.com/bioc/SeqGate", "RemoteRef": "HEAD", "RemoteSha": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-31 10:28:56 UTC", "User": "root" }, "Author": "Christelle Reynès [aut],\nStéphanie Rialle [aut, cre]", "Maintainer": "Stéphanie Rialle ", "_user": "bioc", "_type": "src", "_file": "SeqGate_1.23.0.tar.gz", "_fileid": "https://r2.ropensci.org/0739d27310fa38e787c4ea29f83e8f221cc6172ec7a7576199c90236ca0f49e3", "_filesize": 129881, "_sha256": "0739d27310fa38e787c4ea29f83e8f221cc6172ec7a7576199c90236ca0f49e3", "_expires": "2027-02-08T11:37:57.000Z", "_created": "2026-10-31T10:28:56.000Z", "_published": "2026-10-31T11:37:58.817Z", "_upstream": "https://github.com/bioc/SeqGate", "_status": "success", "_maintainer": { "name": "Stéphanie Rialle", "email": "stephanie.rialle@mgx.cnrs.fr", "login": "srialle", "description": "", "uuid": 37656505 }, "_jobs": [ { "job": 124513316575, "time": 159, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "13039797147" }, { "job": 124513316593, "time": 292, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13039642698" }, { "job": 124513316605, "time": 275, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "13039892117" }, { "job": 124513316596, "time": 125, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13041263582" }, { "job": 124513316578, "time": 193, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13041383023" }, { "job": 124512366225, "time": 254, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "13040005490" }, { "job": 124513316639, "time": 94, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13040080793" }, { "job": 124513316581, "time": 169, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13039367433" }, { "job": 124513316620, "time": 158, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13039537840" }, { "job": 124513316618, "time": 136, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13040075909" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787", "_commit": { "id": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380827 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "S4Vectors", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocManager", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "differentialexpression", "geneexpression", "transcriptomics", "sequencing", "rnaseq" ], "_stars": 0, "_contributors": [ { "user": "srialle", "count": 24, "uuid": 37656505 }, { "user": "nturaga", "count": 2, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 480, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 442, "source": "https://www.bioconductor.org/packages/stats/bioc/SeqGate" }, "_devurl": "https://github.com/srialle/seqgate", "_searchresults": 2, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/SeqGate.html" ], "_homeurl": "https://github.com/srialle/seqgate", "_realowner": "bioc", "_cranurl": false, "_exports": [ "applySeqGate" ], "_datasets": [ { "name": "data_MiTF_1000genes", "title": "Extract of a Transciptome Dataset from Human Melanoma Cell Line", "object": "data_MiTF_1000genes", "file": "data_MiTF_1000genes.rda", "class": [ "data.frame" ], "fields": [ "A1", "A2", "B1", "B2", "A3", "B3" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "SeqGate-package", "title": "Filtering of Lowly Expressed Features", "topics": [ "SeqGate-package", "SeqGate" ] }, { "page": "applySeqGate", "title": "Performs a Filtering of Lowly Expressed Features", "topics": [ "applySeqGate", "seqGate", "seqgate" ] }, { "page": "data_MiTF_1000genes", "title": "Extract of a Transciptome Dataset from Human Melanoma Cell Line", "topics": [ "data_MITF_1000genes", "data_MiTF_1000genes", "data_mitf_1000genes" ] } ], "_rundeps": [ "abind", "Biobase", "BiocGenerics", "BiocManager", "DelayedArray", "generics", "GenomicRanges", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "Seqgate-html-vignette.Rmd", "filename": "Seqgate-html-vignette.html", "title": "SeqGate: Filter lowly expressed features", "author": "Christelle Reynès, Stéphanie Rialle", "engine": "knitr::rmarkdown", "headings": [ "Introduction: SeqGate method description", "Installation", "Filtering with SeqGate", "Input data", "Toy dataset", "Getting the SummarizedExperiment input", "Filtering with default options", "Setting custom filtering parameters", "Parameters detailed explanation", "Custom filtering parameters example", "SessionInfo" ], "created": "2020-07-10 09:07:43", "modified": "2021-01-19 16:01:06", "commits": 6 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "seqgate", "_universes": [ "bioc", "srialle" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-10-31T10:32:25.000Z", "distro": "resolute", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/82e06ba713775abd8f014f6821e1f777e4616fb51cf92f47edf9f61a874b6510", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" }, { "r": "4.6.1", "os": "linux", "version": "1.23.0", "date": "2026-10-31T10:32:20.000Z", "distro": "resolute", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/0b57d87280dbdda979d1ef228f28aef64f1cac2e18ff5e158d3e4ae3701cf0d7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-10-31T11:35:01.000Z", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/00557f3f6a4436e5a057530b41fb4cb4972730dc832d3bc8d880bddbc4ddba53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" }, { "r": "4.6.2", "os": "mac", "version": "1.23.0", "date": "2026-10-31T11:35:53.000Z", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/237be2925c6fbae930205057d87b7f8277ff26e053a894dd74a7dd8a7ec0a309", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-10-31T10:30:59.000Z", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/9779b19022b4219580a0e51a392e41b7646cffcddaa617331500da7f116f4c4a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-10-31T10:30:16.000Z", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/b144d117fa8b5d969041b7dddb0ffa41551e45757aea04e2ef858ca926db4cb4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-10-31T10:30:17.000Z", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/6bd7119e3acdc3f2f9292c1254edbd796ccca30268a9b18b269587a30c6c310a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" }, { "r": "4.6.2", "os": "win", "version": "1.23.0", "date": "2026-10-31T10:30:28.000Z", "commit": "4449ab3582234dba01dd8bcb69faee73364fdaa1", "fileid": "https://r2.ropensci.org/604122068b4d9c9c8c95eaf3d9149d59aae075d8790174eb05c9254582d28c25", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41192564787" } ] }