{ "_id": "6a1ae67e1d7bb097a09f04a6", "Type": "Package", "Package": "ROSeq", "Title": "Modeling expression ranks for noise-tolerant differential\nexpression analysis of scRNA-Seq data", "Version": "1.25.0", "Authors@R": "c(person(\"Krishan\", \"Gupta\", \nemail = \"krishang@iiitd.ac.in\", role = c(\"aut\",\"cre\")),\nperson(\"Manan\", \"Lalit\",\nemail = \"manan.lalit@gmail.com\", role = c(\"aut\")),\nperson(\"Aditya\", \"Biswas\",\nemail = \"Adbiswa@microsoft.com\", role = c(\"aut\")),\nperson(\"Abhik\", \"Ghosh\",\nemail = \"abhianik@gmail.com\", role = c(\"aut\")),\nperson(\"Debarka\", \"Sengupta\",\nemail = \"debarka@gmail.com\", role = c(\"aut\")))", "Description": "ROSeq - A rank based approach to modeling gene expression\nwith filtered and normalized read count matrix. ROSeq takes\nfiltered and normalized read matrix and\ncell-annotation/condition as input and determines the\ndifferentially expressed genes between the contrasting groups\nof single cells. One of the input parameters is the number of\ncores to be used.", "URL": "https://github.com/krishan57gupta/ROSeq", "BugReports": "https://github.com/krishan57gupta/ROSeq/issues", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "biocViews": "GeneExpression, DifferentialExpression, SingleCell", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:35 UTC", "RemoteUrl": "https://github.com/bioc/ROSeq", "RemoteRef": "HEAD", "RemoteSha": "92f6e692c110483e87a35a5972df40ab15f5e71a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:36:45 UTC", "User": "root" }, "Author": "Krishan Gupta [aut, cre],\nManan Lalit [aut],\nAditya Biswas [aut],\nAbhik Ghosh [aut],\nDebarka Sengupta [aut]", "Maintainer": "Krishan Gupta ", "MD5sum": "41dc12dd785229af03b53c62243087fa", "_user": "bioc", "_type": "src", "_file": "ROSeq_1.25.0.tar.gz", "_fileid": "e230172729d53d87ea631eceb061aad09ffc80362f124dfc81e874fa250ebbe2", "_filesize": 4516443, "_sha256": "e230172729d53d87ea631eceb061aad09ffc80362f124dfc81e874fa250ebbe2", "_created": "2026-05-30T09:36:45.000Z", "_published": "2026-05-30T13:30:38.746Z", "_jobs": [ { "job": 78640083328, "time": 139, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307325651" }, { "job": 78640083341, "time": 398, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307349331" }, { "job": 78640083349, "time": 340, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307344673" }, { "job": 78640083353, "time": 167, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308516513" }, { "job": 78640083354, "time": 201, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308523586" }, { "job": 78639407835, "time": 300, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307227039" }, { "job": 78640083336, "time": 104, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307321735" }, { "job": 78640083352, "time": 403, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307343678" }, { "job": 78640083355, "time": 341, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307339478" }, { "job": 78640083351, "time": 334, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307338749" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ROSeq", "_commit": { "id": "92f6e692c110483e87a35a5972df40ab15f5e71a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380755 }, "_maintainer": { "name": "Krishan Gupta", "email": "krishang@iiitd.ac.in", "login": "krishan57gupta", "description": "I am a research scholar working with the advisor Dr Debarka Sengupta, Computer Science and Center for Computational Biology Department, IIIT Delhi.", "uuid": 26205662 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "pbmcapply", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "differentialexpression", "singlecell", "count-data", "gene-expression", "gene-expression-profiles", "normalization", "populations", "rank", "tmm", "tung", "tung-dataset", "tutorial", "vignette" ], "_stars": 2, "_contributors": [ { "user": "krishan57gupta-star", "count": 303, "uuid": 267823780 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 369, "source": "https://www.bioconductor.org/packages/stats/bioc/ROSeq" }, "_devurl": "https://github.com/krishan57gupta/roseq", "_searchresults": 19, "_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/ROSeq.html", "manual.pdf" ], "_homeurl": "https://github.com/krishan57gupta/roseq", "_realowner": "bioc", "_cranurl": false, "_exports": [ "ROSeq", "TMMnormalization" ], "_datasets": [ { "name": "L_Tung_single", "title": "Single cell samples for DE genes analysis", "object": "L_Tung_single", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "computeDEG", "title": "Computes differential expression for the gene in question, by comparing the optimal parameters for sub-populations one and two", "topics": [ "computeDEG" ] }, { "page": "findParams", "title": "Finds the optimal values of parameters a and b that model the probability distribution of ranks, by Maximising the Log-Likelihood", "topics": [ "findParams" ] }, { "page": "getd", "title": "Finds the double derivative of A", "topics": [ "getd" ] }, { "page": "getDataStatistics", "title": "Evaluates statistics of the read counts corresponding to the gene", "topics": [ "getDataStatistics" ] }, { "page": "getdu1da", "title": "Finds the first derivative of u1 with respect to a. This first derivative is evaluated at the optimal (a_hat, b_hat).", "topics": [ "getdu1da" ] }, { "page": "getdu1db", "title": "Finds the first derivative of u1 with respect to b. This first derivative is evaluated at the optimal (a_hat, b_hat).", "topics": [ "getdu1db" ] }, { "page": "getdu2da", "title": "Finds the first derivative of u2 with respect to a. This first derivative is evaluated at the optimal (a_hat, b_hat).", "topics": [ "getdu2da" ] }, { "page": "getdu2db", "title": "Finds the first derivative of u2 with respect to b. This first derivative is evaluated at the optimal (a_hat, b_hat).", "topics": [ "getdu2db" ] }, { "page": "getdvda", "title": "Finds the first derivative of v with respect to a. This first derivative is evaluated at the optimal (a_hat, b_hat).", "topics": [ "getdvda" ] }, { "page": "getdvdb", "title": "Finds the first derivative of v with respect to b. This first derivative is evaluated at the optimal (a_hat, b_hat).", "topics": [ "getdvdb" ] }, { "page": "getI", "title": "Computes the Fisher Information Matrix", "topics": [ "getI" ] }, { "page": "getu1", "title": "Computes u1", "topics": [ "getu1" ] }, { "page": "getu2", "title": "Computes u2", "topics": [ "getu2" ] }, { "page": "getv", "title": "Computes v", "topics": [ "getv" ] }, { "page": "initiateAnalysis", "title": "Computes differential analysis for a given gene", "topics": [ "initiateAnalysis" ] }, { "page": "L_Tung_single", "title": "Single cell samples for DE genes analysis", "topics": [ "L_Tung_single" ] }, { "page": "minimizeNLL", "title": "Minimizes the Negative Log-Likelihood by iterating across values of parameters a and b", "topics": [ "minimizeNLL" ] }, { "page": "ROSeq", "title": "Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data", "topics": [ "ROSeq" ] }, { "page": "TMMnormalization", "title": "TMM Normalization.", "topics": [ "TMMnormalization" ] } ], "_readme": "https://github.com/bioc/ROSeq/raw/HEAD/README.md", "_rundeps": [ "edgeR", "lattice", "limma", "locfit", "pbmcapply", "statmod" ], "_vignettes": [ { "source": "ROSeq.Rmd", "filename": "ROSeq.html", "title": "ROSeq", "engine": "knitr::rmarkdown", "headings": [ "ROSeq", "Introduction", "Installation", "Vignette tutorial", "Example", "Loading tung dataset", "Data Preprocessing:", "Cells and genes filtering then voom transformation after TMM normalization", "ROSeq analysis.", "Showing results are in the form of pVals and pAdj", "p_Vals : p_value (unadjusted)", "p_Adj : Adjusted p-value, based on FDR method" ], "created": "2019-12-04 16:41:51", "modified": "2021-02-16 18:03:27", "commits": 24 } ], "_score": 4.57978359661681, "_indexed": true, "_nocasepkg": "roseq", "_universes": [ "bioc", "krishan57gupta" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T09:54:40.000Z", "distro": "noble", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "bcdaf96db1e0f120e26fde52696e3c935441ae8fcc3c6c7f4e67ed80ade79b7a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T09:53:54.000Z", "distro": "noble", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "4227cd0d8d6cc93195317505c0d267bc6a2b9aaf3e6dbe80697f63425057c24d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-30T13:27:15.000Z", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "4c1eecf78bdf90e0e7a175cbc9c3c8fc076472ea885cf98d6fabed28e72d8dfd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-30T13:28:13.000Z", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "83055eeb8ae4ffbf5521934c23aa80c6fd037bbcb182f83f61d4d89df67d9fa0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-30T09:52:41.000Z", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "54b63ae3b8368c807f0cc632687dca9eae32127787e0da7d607676f86e48801c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T09:50:48.000Z", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "ab7a529401f40c7ae251ba7eb6686348ed4b9d37d5584f25564c96b9c4ec8b41", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-30T09:51:00.000Z", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "99545e1c52489cce99e264a239aeed5f9d0e441f0dce535c8f87706e3472037f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T09:51:02.000Z", "commit": "92f6e692c110483e87a35a5972df40ab15f5e71a", "fileid": "668b546044ed6984ddc4b19a84d1cd97af4f6e7946d471448ea96cdc09800923", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675789460" } ] }