{ "_id": "6ac8da94de46216d5edd8718", "Package": "NetActivity", "Type": "Package", "Title": "Compute gene set scores from a deep learning framework", "Version": "1.15.0", "Authors@R": "c(person(\"Carlos\", \"Ruiz-Arenas\", , \"carlos.ruiza@upf.edu\", role = c(\"aut\", \"cre\")))", "Description": "#' NetActivity enables to compute gene set scores from\npreviously trained sparsely-connected autoencoders. The package\ncontains a function to prepare the data\n(`prepareSummarizedExperiment`) and a function to compute the\ngene set scores (`computeGeneSetScores`). The package\n`NetActivityData` contains different pre-trained models to be\ndirectly applied to the data. Alternatively, the users might\nuse the package to compute gene set scores using custom models.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Config/testthat/edition": "3", "biocViews": "RNASeq, Microarray, Transcription, FunctionalGenomics, GO,\nGeneExpression, Pathways, Software", "RoxygenNote": "7.2.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:59:23 UTC", "RemoteUrl": "https://github.com/bioc/NetActivity", "RemoteRef": "HEAD", "RemoteSha": "0e261497beadffad703b9eddaabca33b2a0460a4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-09 12:05:28 UTC", "User": "root" }, "Author": "Carlos Ruiz-Arenas [aut, cre]", "Maintainer": "Carlos Ruiz-Arenas ", "_user": "bioc", "_type": "src", "_file": "NetActivity_1.15.0.tar.gz", "_fileid": "https://r2.ropensci.org/a3d8771ef7040d67cae3a5fa9c72124283017148169bafb99d06604b54e801ac", "_filesize": 234566, "_sha256": "a3d8771ef7040d67cae3a5fa9c72124283017148169bafb99d06604b54e801ac", "_expires": "2027-01-17T12:14:10.000Z", "_created": "2026-10-09T12:05:28.000Z", "_published": "2026-10-09T12:14:12.101Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_upstream": "https://github.com/bioc/NetActivity", "_commit": { "id": "0e261497beadffad703b9eddaabca33b2a0460a4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381163 }, "_maintainer": { "name": "Carlos Ruiz-Arenas", "email": "carlos.ruiza@upf.edu" }, "_distro": "resolute", "_jobs": [ { "job": 113811017785, "time": 200, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11614394684" }, { "job": 113811017552, "time": 466, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11614951919" }, { "job": 113811017595, "time": 418, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11614798177" }, { "job": 113811017637, "time": 284, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11615151379" }, { "job": 113811017601, "time": 305, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11614901620" }, { "job": 113809134475, "time": 322, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11615050666" }, { "job": 113811017702, "time": 169, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11614574173" }, { "job": 113811017765, "time": 314, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11614852661" }, { "job": 113811017684, "time": 319, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11615211418" }, { "job": 113811017653, "time": 295, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11615266185" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "airway", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "DelayedMatrixStats", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "NetActivityData", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "Fletcher2013a", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.15.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "rnaseq", "microarray", "transcription", "functionalgenomics", "go", "geneexpression", "pathways", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 475, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 368, "source": "https://www.bioconductor.org/packages/stats/bioc/NetActivity" }, "_searchresults": 33, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NetActivity.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "computeGeneSetScores", "prepareSummarizedExperiment" ], "_help": [ { "page": "computeGeneSetScores", "title": "Compute gene set scores", "topics": [ "computeGeneSetScores" ] }, { "page": "NetActivity", "title": "NetActivity: compute gene set scores from a deep learning framework", "topics": [ "NetActivity" ] }, { "page": "prepareSummarizedExperiment", "title": "Prepare a SummarizedExperiment for computing gene set scores computation", "topics": [ "prepareSummarizedExperiment" ] } ], "_readme": "https://github.com/bioc/NetActivity/raw/HEAD/README.md", "_rundeps": [ "abind", "airway", "BH", "Biobase", "BiocGenerics", "BiocParallel", "cli", "codetools", "cpp11", "DelayedArray", "DelayedMatrixStats", "DESeq2", "farver", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lambda.r", "lattice", "lifecycle", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "NetActivityData", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "sparseMatrixStats", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "NetActivity.Rmd", "filename": "NetActivity.html", "title": "Gene set scores computation with NetActivity", "author": "Carlos Ruiz Arenas", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Introduction", "Pre-processing", "RNAseq", "Microarray data", "Computing the scores", "Differential gene set scores analysis" ], "created": "2022-09-13 08:22:20", "modified": "2022-10-17 14:02:17", "commits": 5 } ], "_score": 4.518513939877888, "_indexed": true, "_nocasepkg": "netactivity", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-10-09T12:11:10.000Z", "distro": "resolute", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/a7893fd8b722c8426f1e42028bd5bd89f68f87245d15c82b3dba735a37ed731e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" }, { "r": "4.6.1", "os": "linux", "version": "1.15.0", "date": "2026-10-09T12:10:21.000Z", "distro": "resolute", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/fd3defaacaa9e3f1fb1d3369621b427f31d256f5882546785d8d297d86248e6b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-10-09T12:08:10.000Z", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/ca40488cf8fd242eca337d9b16fc78466ec7a1924175ada7cee96b66287bd1bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" }, { "r": "4.6.1", "os": "mac", "version": "1.15.0", "date": "2026-10-09T12:08:14.000Z", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/eb41f69ee36d4313e0b82179fb5501b7e6e1a1b7baefd4ed1a024ebb3f560dde", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-10-09T12:08:49.000Z", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/34ca92bbcea826f2c037e3a7e9c3fcb5a7d0244bc17fcfe2efc6f091a46b04c7", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-10-09T12:08:26.000Z", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/a5cf78183bab8b43ef847bca5a178064530d114e6ee2a3cfdf6472886a31d785", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-10-09T12:08:43.000Z", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/4cfce8df0301dfd64cb9961e698d57e1fcbf080a33871cf2f97084fb08e8c2a2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" }, { "r": "4.6.1", "os": "win", "version": "1.15.0", "date": "2026-10-09T12:08:16.000Z", "commit": "0e261497beadffad703b9eddaabca33b2a0460a4", "fileid": "https://r2.ropensci.org/9e8e66863c4092ecd749a50d05ddf9db960295b509d960949cd8202ab24efdff", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927245907" } ] }