{ "_id": "6a102562acfb0bcc41c8eb1d", "Package": "awst", "Title": "Asymmetric Within-Sample Transformation", "Version": "1.21.0", "Authors@R": "c(person(given = \"Davide\",\nfamily = \"Risso\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"risso.davide@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8508-5012\")),\nperson(given = \"Stefano\",\nfamily = \"Pagnotta\",\nrole = c(\"aut\", \"cph\"),\nemail = \"smpagnotta@gmail.com\",\ncomment = c(ORCID = \"0000-0002-8298-9777\")))", "Description": "We propose an Asymmetric Within-Sample Transformation\n(AWST) to regularize RNA-seq read counts and reduce the effect\nof noise on the classification of samples. AWST comprises two\nmain steps: standardization and smoothing. These steps\ntransform gene expression data to reduce the noise of the lowly\nexpressed features, which suffer from background effects and\nlow signal-to-noise ratio, and the influence of the highly\nexpressed features, which may be the result of amplification\nbias and other experimental artifacts.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "URL": "https://github.com/drisso/awst", "BugReports": "https://github.com/drisso/awst/issues", "biocViews": "Normalization, GeneExpression, RNASeq, Software,\nTranscriptomics, Sequencing, SingleCell", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:53 UTC", "RemoteUrl": "https://github.com/bioc/awst", "RemoteRef": "HEAD", "RemoteSha": "c693f862908ad025a3a1220f0a0528293bf25006", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 09:38:10 UTC", "User": "root" }, "Author": "Davide Risso [aut, cre, cph] (ORCID:\n),\nStefano Pagnotta [aut, cph] (ORCID:\n)", "Maintainer": "Davide Risso ", "MD5sum": "423e0dc58edd6566e4d0b7d41c0cfff3", "_user": "bioc", "_type": "src", "_file": "awst_1.21.0.tar.gz", "_fileid": "6997df89743a936658528b33f0397392eac6e639296f8f37024bf6725888421b", "_filesize": 223397, "_sha256": "6997df89743a936658528b33f0397392eac6e639296f8f37024bf6725888421b", "_created": "2026-05-22T09:38:10.000Z", "_published": "2026-05-22T09:44:01.993Z", "_jobs": [ { "job": 77354616708, "time": 189, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7157512948" }, { "job": 77354616625, "time": 300, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7157546932" }, { "job": 77354616768, "time": 296, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7157545781" }, { "job": 77354616618, "time": 170, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7157506870" }, { "job": 77354616647, "time": 198, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7157515536" }, { "job": 77353903789, "time": 290, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7157456296" }, { "job": 77354616631, "time": 170, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7157506958" }, { "job": 77354616643, "time": 236, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7157527259" }, { "job": 77354616661, "time": 211, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7157519432" }, { "job": 77354616657, "time": 210, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7157518977" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 3 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/awst", "_commit": { "id": "c693f862908ad025a3a1220f0a0528293bf25006", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380953 }, "_maintainer": { "name": "Davide Risso", "email": "risso.davide@gmail.com", "login": "drisso", "description": "", "uuid": 8451432, "orcid": "0000-0001-8508-5012" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "airway", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "EDASeq", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "RefManageR", "role": "Suggests" }, { "package": "sessioninfo", "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": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "normalization", "geneexpression", "rnaseq", "software", "transcriptomics", "sequencing", "singlecell" ], "_stars": 3, "_contributors": [ { "user": "drisso", "count": 42, "uuid": 8451432 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 403, "source": "https://www.bioconductor.org/packages/stats/bioc/awst" }, "_devurl": "https://github.com/drisso/awst", "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/awst.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/drisso/awst", "_realowner": "bioc", "_cranurl": false, "_exports": [ "awst", "gene_filter" ], "_help": [ { "page": "awst", "title": "Asymmetric Within-Sample Transformation", "topics": [ "awst", "awst,matrix-method", "awst,SummarizedExperiment-method" ] }, { "page": "gene_filter", "title": "Gene filtering based on heterogeneity", "topics": [ "gene_filter", "gene_filter,matrix-method", "gene_filter,SummarizedExperiment-method" ] } ], "_readme": "https://github.com/bioc/awst/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "DelayedArray", "generics", "GenomicRanges", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "awst_intro.Rmd", "filename": "awst_intro.html", "title": "Introduction to awst", "author": "Davide Risso", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Install awst", "Required knowledge", "Asking for help", "Citing awst", "What does awst does?", "Quick start", "Role of normalization", "Reproducibility", "Bibliography" ], "created": "2021-04-14 10:47:47", "modified": "2021-05-04 16:30:24", "commits": 4 } ], "_score": 4.954242509439325, "_indexed": true, "_nocasepkg": "awst", "_universes": [ "bioc", "drisso" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-22T09:41:51.000Z", "distro": "noble", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "d836c1fbb98fa0decad1e84b53e19910e695b8415fe050f4c8f82cf53570c9ed", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-22T09:41:47.000Z", "distro": "noble", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "fb4a3c5f2180004b0a71f53017779ed8b192f0ff655d51d7a7ee8af2c9dae6ed", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-22T09:40:11.000Z", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "73678cec0c44e24bae40b4b474a7fc0f3a157f366dbcbec21a635d3a742eb741", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-22T09:40:27.000Z", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "b1f58d59dbec361fd8a608a7aa392666294c7a8abf996a3ae672a326fd2f0d19", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-22T09:41:28.000Z", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "e74b659b1a4b617be945b4c5c196091f0366fda5f5f26ecfa01c7413de927779", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-22T09:40:59.000Z", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "9236f52843ea78ae345e8dfda398df822b42234543dd75ecf97e7837f6b9d4a4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-22T09:40:22.000Z", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "568348debc465c870b3559bf4b8195ec04a2120198a879a2f2ec3b3fa37db30e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-22T09:40:13.000Z", "commit": "c693f862908ad025a3a1220f0a0528293bf25006", "fileid": "5e538ec8484b6caed540b00913a36574f8a57a60cbf02df16d9ee588212fe674", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280100954" } ] }