{ "_id": "6aca77bffe5cc25786e89b27", "Package": "SDAMS", "Type": "Package", "Title": "Differential Abundant/Expression Analysis for Metabolomics,\nProteomics and single-cell RNA sequencing Data", "Version": "1.33.0", "Date": "2023-07-21", "Author": "Yuntong Li , Chi Wang\n, Li Chen ", "Maintainer": "Yuntong Li ", "Description": "This Package utilizes a Semi-parametric Differential\nAbundance/expression analysis (SDA) method for metabolomics and\nproteomics data from mass spectrometry as well as single-cell\nRNA sequencing data. SDA is able to robustly handle\nnon-normally distributed data and provides a clear\nquantification of the effect size.", "License": "GPL", "LazyLoad": "no", "NeedsCompilation": "no", "biocViews": "ImmunoOncology, DifferentialExpression, Metabolomics,\nProteomics, MassSpectrometry, SingleCell", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:47:48 UTC", "RemoteUrl": "https://github.com/bioc/SDAMS", "RemoteRef": "HEAD", "RemoteSha": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "Packaged": { "Date": "2026-10-10 16:03:06 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "SDAMS_1.33.0.tar.gz", "_fileid": "https://r2.ropensci.org/c8abbe45da99bd3a67ce21c59cf8ae2c423db10d4c5b97932ab45664e6145777", "_filesize": 1358249, "_sha256": "c8abbe45da99bd3a67ce21c59cf8ae2c423db10d4c5b97932ab45664e6145777", "_expires": "2027-01-18T17:37:00.000Z", "_created": "2026-10-10T16:03:06.000Z", "_published": "2026-10-10T17:37:02.927Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 2, "warning": 3, "note": 9 }, "_upstream": "https://github.com/bioc/SDAMS", "_commit": { "id": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380468 }, "_maintainer": { "name": "Yuntong Li", "email": "liyuntong0704@gmail.com", "login": "stat-li", "description": "", "uuid": 36005627 }, "_distro": "resolute", "_jobs": [ { "job": 114254013926, "time": 162, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11675063633" }, { "job": 114254013869, "time": 321, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11674709397" }, { "job": 114254013908, "time": 267, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11674278556" }, { "job": 114254013928, "time": 199, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11677460833" }, { "job": 114254013899, "time": 254, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11677178687" }, { "job": 114253194084, "time": 239, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11675088302" }, { "job": 114254013878, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11674524596" }, { "job": 114254013983, "time": 252, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11674789176" }, { "job": 114254013906, "time": 228, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11674348510" }, { "job": 114254013907, "time": 233, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11675148594" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "trust", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.33.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.32.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "differentialexpression", "metabolomics", "proteomics", "massspectrometry", "singlecell" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 470, "source": "https://www.bioconductor.org/packages/stats/bioc/SDAMS" }, "_mentions": 2, "_searchresults": 1, "_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/SDAMS.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "createSEFromCSV", "createSEFromMatrix", "SDA" ], "_datasets": [ { "name": "exampleSingleCell", "title": "Two example datasets for SDAMS package", "object": "exampleSingleCell", "file": "exampleSingleCell.rda", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "exampleSumExp", "title": "Two example datasets for SDAMS package", "object": "exampleSumExp", "file": "exampleSumExp.rda", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "SDAMS-package", "title": "SDAMS package for differential abundance/expression analysis of Metabolomics, Proteomics and single-cell RNA sequencing data", "topics": [ "SDAMS-package" ] }, { "page": "dataInput", "title": "Mass spectrometry data input", "topics": [ "createSEFromCSV", "createSEFromMatrix", "dataInput" ] }, { "page": "exampleData", "title": "Two example datasets for SDAMS package", "topics": [ "exampleData", "exampleSingleCell", "exampleSumExp" ] }, { "page": "SDA", "title": "Semi-parametric differential abuandance/expression analysis", "topics": [ "SDA" ] } ], "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "plyr", "qvalue", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "trust", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "SDAMS.Rnw", "filename": "SDAMS.pdf", "title": "SDAMS Vignette", "engine": "utils::Sweave", "headings": [ "1 Citation", "2 Quick Start", "3 Data Input", "4 Data Analysis", "5 Theory for SDAMS", "6 Session Info" ], "created": "2018-02-01 01:53:48", "modified": "2023-07-26 14:11:02", "commits": 17 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "sdams", "_universes": [ "bioc", "stat-li" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.33.0", "date": "2026-10-10T16:06:14.000Z", "distro": "resolute", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/3e1f9cf9e1d49864a695697b145c022768daa2f35d3383887d6a614fabbb5dd9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" }, { "r": "4.6.1", "os": "linux", "version": "1.33.0", "date": "2026-10-10T16:05:44.000Z", "distro": "resolute", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/7868db066f1d62616a285f2d7b673d489a3472258b1050f572bc4992576e9537", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" }, { "r": "4.5.3", "os": "mac", "version": "1.33.0", "date": "2026-10-10T17:33:58.000Z", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/2aceaffbc1c4f7905f6cde75237fcb8b46104ec36320ce56ab94142455f1e2e0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" }, { "r": "4.6.1", "os": "mac", "version": "1.33.0", "date": "2026-10-10T17:33:58.000Z", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/47b2aa2474f0b504c408e90d992b09f253e891fd82757eb6952720298ecdc6dd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" }, { "r": "4.6.0", "os": "wasm", "version": "1.33.0", "date": "2026-10-10T16:05:21.000Z", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/aec48064df59bda751608ca71ebeb2ca05c43746bad80d4d9ca466a154a92d5e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" }, { "r": "4.7.0", "os": "win", "version": "1.33.0", "date": "2026-10-10T16:04:35.000Z", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/f0382290f2e17d1aa76e22e8fabb715510472126d96f76f5cdad78ae15855dd5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" }, { "r": "4.5.3", "os": "win", "version": "1.33.0", "date": "2026-10-10T16:04:37.000Z", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/149fb902c1d1fd6b2cd105a8391153b1f5ccaa8c6c89c8c576c58748e85db6f5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" }, { "r": "4.6.1", "os": "win", "version": "1.33.0", "date": "2026-10-10T16:04:34.000Z", "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e", "fileid": "https://r2.ropensci.org/00ee2794975346b2335e06fc8ef22a706d36b827348e27502435541c0d10f927", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38065823201" } ] }