{ "_id": "6ad601c76b811b735aabe187", "Package": "SiPSiC", "Type": "Package", "Title": "Calculate Pathway Scores for Each Cell in scRNA-Seq Data", "Version": "1.13.0", "Date": "2022-12-29", "Authors@R": "c(person(\"Daniel\", \"Davis\", role = c(\"aut\", \"cre\"), email=\"DanielDavis000@gmail.com\", comment=c(ORCID=\"0000-0001-7863-1521\")),\nperson(\"Yotam\", \"Drier\", role = \"aut\"))", "Description": "Infer biological pathway activity of cells from\nsingle-cell RNA-sequencing data by calculating a pathway score\nfor each cell (pathway genes are specified by the user). It is\nrecommended to have the data in Transcripts-Per-Million (TPM)\nor Counts-Per-Million (CPM) units for best results. Scores may\nchange when adding cells to or removing cells off the data.\nSiPSiC stands for Single Pathway analysis in Single Cells.", "License": "file LICENSE", "URL": "https://www.genome.org/cgi/doi/10.1101/gr.278431.123", "biocViews": "Software, DifferentialExpression, GeneSetEnrichment,\nBiomedicalInformatics, CellBiology, Transcriptomics, RNASeq,\nSingleCell, Transcription, Sequencing, ImmunoOncology,\nDataImport", "VignetteBuilder": "knitr", "BugReports": "https://github.com/DanielDavis12/SiPSiC/issues", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:00:29 UTC", "RemoteUrl": "https://github.com/bioc/SiPSiC", "RemoteRef": "HEAD", "RemoteSha": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-19 11:33:01 UTC", "User": "root" }, "Author": "Daniel Davis [aut, cre] (ORCID:\n),\nYotam Drier [aut]", "Maintainer": "Daniel Davis ", "_user": "bioc", "_type": "src", "_file": "SiPSiC_1.13.0.tar.gz", "_fileid": "https://r2.ropensci.org/88d47ade13f918ef5d6f13d0ca9ce35f6060bda437056d344dcb67d9db2cd4bf", "_filesize": 113861, "_sha256": "88d47ade13f918ef5d6f13d0ca9ce35f6060bda437056d344dcb67d9db2cd4bf", "_expires": "2027-01-27T11:40:53.000Z", "_created": "2026-10-19T11:33:01.000Z", "_published": "2026-10-19T11:40:55.552Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_upstream": "https://github.com/bioc/SiPSiC", "_commit": { "id": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381229 }, "_maintainer": { "name": "Daniel Davis", "email": "danieldavis000@gmail.com", "login": "danieldavis12", "description": "", "uuid": 122206202, "orcid": "0000-0001-7863-1521" }, "_distro": "resolute", "_jobs": [ { "job": 118036335851, "time": 307, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12182664659" }, { "job": 118036335888, "time": 267, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12183193235" }, { "job": 118036335893, "time": 388, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12184060316" }, { "job": 118036335773, "time": 163, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12182509631" }, { "job": 118036335776, "time": 160, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12182767440" }, { "job": 118033963668, "time": 358, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12183041557" }, { "job": 118036335735, "time": 272, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12184065035" }, { "job": 118036335927, "time": 191, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12182832316" }, { "job": 118036335990, "time": 181, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12182484842" }, { "job": 118036335895, "time": 415, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12183248565" } ], "_registered": true, "_dependencies": [ { "package": "Matrix", "role": "Depends" }, { "package": "SingleCellExperiment", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.13.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.12.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "differentialexpression", "genesetenrichment", "biomedicalinformatics", "cellbiology", "transcriptomics", "rnaseq", "singlecell", "transcription", "sequencing", "immunooncology", "dataimport" ], "_stars": 8, "_contributors": [ { "user": "danieldavis12", "count": 41, "uuid": 122206202 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 478, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 339, "source": "https://www.bioconductor.org/packages/stats/bioc/SiPSiC" }, "_devurl": "https://github.com/danieldavis12/sipsic", "_searchresults": 11, "_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/readme.html", "extra/readme.md", "extra/SiPSiC.html", "LICENSE" ], "_homeurl": "https://github.com/danieldavis12/sipsic", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getPathwayScores" ], "_help": [ { "page": "SiPSiC-package", "title": "Calculate Pathway Scores for Each Cell in scRNA-Seq Data", "topics": [ "SiPSiC-package", "SiPSiC" ] }, { "page": "getPathwayScores", "title": "Calculate Pathway Scores for all Cells in a scRNA-Seq Data", "topics": [ "getPathwayScores" ] }, { "page": "SiPSiC-internal", "title": "Gene counts normalization", "topics": [ "normalizeCountsForGene" ] } ], "_readme": "https://github.com/bioc/SiPSiC/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "DelayedArray", "generics", "GenomicRanges", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "SiPSiC.Rmd", "filename": "SiPSiC.html", "title": "SiPSiC - Infer Biological Pathway Activity from Single-Cell RNA-Seq Data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Code Example", "SiPSiC's Algorithm", "1. Pathway data extraction", "2. Score normalization", "3. Normalized gene rankings calculation", "4. Gene weighing", "5. Pathway scoring", "Session Information" ], "created": "2023-01-09 09:30:26", "modified": "2023-12-11 11:12:42", "commits": 6 } ], "_score": 5.421603926869831, "_indexed": true, "_nocasepkg": "sipsic", "_universes": [ "bioc", "danieldavis12" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13.0", "date": "2026-10-19T11:36:04.000Z", "distro": "resolute", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/0227816e09382969d473d619752055550b3dac8bb0fbc49a3436914ca8073e49", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" }, { "r": "4.6.1", "os": "linux", "version": "1.13.0", "date": "2026-10-19T11:38:13.000Z", "distro": "resolute", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/6e6fac50ffa113c844ed5a9f55358e72e73fc7160811a5b2c4247bd922fe7379", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" }, { "r": "4.5.3", "os": "mac", "version": "1.13.0", "date": "2026-10-19T11:35:02.000Z", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/a93e528bc5aa5bde3f089c9f233e4c50856c40d3477cabdde529044554ae3213", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" }, { "r": "4.6.1", "os": "mac", "version": "1.13.0", "date": "2026-10-19T11:34:55.000Z", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/3d1d742223c102ddef7ae5f5be3ffd43f5bdf2cc02c842a68727adde93c59a3f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" }, { "r": "4.6.0", "os": "wasm", "version": "1.13.0", "date": "2026-10-19T11:38:02.000Z", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/8cd1a7774698178c59125b18a94618eaaf8c5bcb7f3c48f5daccd61c5da62ca1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" }, { "r": "4.7.0", "os": "win", "version": "1.13.0", "date": "2026-10-19T11:34:35.000Z", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/c104be8b0840c3ad6250f7ccdb5b1821722e1efc3fd450ac4dab3045ec650138", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" }, { "r": "4.5.3", "os": "win", "version": "1.13.0", "date": "2026-10-19T11:34:33.000Z", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/eec12ea866d74e03a776134b7dad2ebd598863b9512a7f24fb70e749fe326990", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" }, { "r": "4.6.1", "os": "win", "version": "1.13.0", "date": "2026-10-19T11:38:27.000Z", "commit": "ee7c0723f877c7e4fdc58b6b2297b549142e0e86", "fileid": "https://r2.ropensci.org/883d4e0e2c043831f8c6a7eb11444528dc847c60e96715f39fa18028fced417c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39244740406" } ] }