{ "_id": "6a47c56ce06c18f0a651dde4", "Package": "SAVER", "Type": "Package", "Version": "1.1.3", "Title": "Single-Cell RNA-Seq Gene Expression Recovery", "Description": "An implementation of a regularized regression prediction\nand empirical Bayes method to recover the true gene expression\nprofile in noisy and sparse single-cell RNA-seq data. See Huang\nM, et al (2018) for more\ndetails.", "Authors@R": "c(\nperson(\"Mo\", \"Huang\", email = \"mohuangx@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Nancy\", \"Zhang\", email = \"nzh@wharton.upenn.edu\", role = \"aut\"),\nperson(\"Mingyao\", \"Li\", email = \"mingyao@pennmedicine.upenn.edu\",\nrole = \"aut\")\n)", "Maintainer": "Mo Huang ", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.0", "URL": "https://github.com/mohuangx/SAVER", "BugReports": "https://github.com/mohuangx/SAVER/issues", "VignetteBuilder": "knitr", "Repository": "https://mohuangx.r-universe.dev", "Date/Publication": "2024-11-28 01:28:02 UTC", "RemoteUrl": "https://github.com/mohuangx/saver", "RemoteRef": "HEAD", "RemoteSha": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 14:17:56 UTC", "User": "root" }, "Author": "Mo Huang [aut, cre],\nNancy Zhang [aut],\nMingyao Li [aut]", "_user": "mohuangx", "_type": "src", "_file": "SAVER_1.1.3.tar.gz", "_fileid": "https://r2.ropensci.org/5d03e9c67c97570ecca66a0623046b2b47f4bb0d4d03ce9dec9a4acc44a7f6dd", "_filesize": 3093162, "_sha256": "5d03e9c67c97570ecca66a0623046b2b47f4bb0d4d03ce9dec9a4acc44a7f6dd", "_expires": "2026-10-11T14:21:30.000Z", "_created": "2026-07-03T14:17:56.000Z", "_published": "2026-07-03T14:21:32.351Z", "_jobs": [ { "job": 85018742838, "time": 135, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8068824870" }, { "job": 85018742844, "time": 119, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8068819849" }, { "job": 85018742864, "time": 136, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8068816631" }, { "job": 85018742849, "time": 180, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8068830837" }, { "job": 85018309997, "time": 152, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8068777925" }, { "job": 85018742854, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8068825157" }, { "job": 85018742860, "time": 83, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8068807292" }, { "job": 85018742862, "time": 119, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8068819713" }, { "job": 85018742882, "time": 76, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8068805134" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613", "_status": "success", "_upstream": "https://github.com/mohuangx/saver", "_commit": { "id": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "author": "Mo Huang ", "committer": "Mo Huang ", "message": "Update to MIT license\n", "time": 1732757282 }, "_maintainer": { "name": "Mo Huang", "email": "mohuangx@gmail.com", "login": "mohuangx", "description": "Associate Director, Biostatistics at Pfizer", "uuid": 26659687 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.1", "role": "Depends" }, { "package": "glmnet", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "iterators", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "mohuangx", "_selfowned": true, "_usedby": 2, "_updates": [], "_tags": [], "_stars": 116, "_contributors": [ { "user": "mohuangx", "count": 48, "uuid": 26659687 } ], "_userbio": { "uuid": 26659687, "type": "user", "name": "Mo Huang", "followers": 21, "description": "Associate Director, Biostatistics at Pfizer" }, "_downloads": { "count": 441, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SAVER" }, "_mentions": 40, "_devurl": "https://github.com/mohuangx/saver", "_searchresults": 267, "_rbuild": "4.6.1", "_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/SAVER.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/mohuangx/saver", "_realowner": "mohuangx", "_cranurl": true, "_releases": [ { "version": "1.1.1", "date": "2018-10-14" }, { "version": "1.1.2", "date": "2019-11-13" } ], "_exports": [ "calc.a", "calc.b", "calc.estimate", "calc.estimate.mean", "calc.estimate.null", "calc.k", "calc.loglik.a", "calc.loglik.b", "calc.loglik.k", "calc.maxcor", "calc.post", "combine.saver", "cor.cells", "cor.genes", "expr.predict", "get.mu", "sample.saver", "saver", "saver.fit", "saver.fit.mean", "saver.fit.null" ], "_datasets": [ { "name": "linnarsson", "title": "Mouse brain single-cell RNA-seq dataset", "object": "linnarsson", "class": [ "matrix", "array" ], "fields": [ "1772071015_C02", "1772071017_G12", "1772071017_A05", "1772071014_B06", "1772067065_H06", "1772071017_E02", "1772067065_B07", "1772067060_B09", "1772071014_E04", "1772071015_D04", "1772071015_C11", "1772071017_D04", "1772071017_D06", "1772067082_D07", "1772071017_F09", "1772071017_A09", "1772067094_C05", "1772067059_B06", "1772067096_E05", "1772066089_C05", "1772067094_F04", "1772071045_A01", "1772071015_C08", "1772071045_D06", "1772071017_A03", "1772071017_F07", "1772071017_E06", "1772067066_C10", "1772071017_B05", "1772071014_E06", "1772067058_D11", "1772071014_B04", "1772067066_B09", "1772071017_E10", "1772071015_B08", "1772071014_C11", "1772067066_E10", "1772067065_F11", "1772071014_H11", "1772071017_B11", "1772071014_A07", "1772071017_B03", "1772071015_B04", "1772071014_D03", "1772067065_D06", "1772067066_H08", "1772067096_G11", "1772071017_G11", "1772067054_E12", "1772067083_B12", "1772067054_G01", "1772067096_A02", "1772067083_B09", "1772071014_H12", "1772067082_H11", "1772067094_D06", "1772071015_F03", "1772071015_B11", "1772071014_G10", "1772067066_B07", "1772067065_G01", "1772071015_F07", "1772067065_E07", "1772071015_C10", "1772067063_E06", "1772067065_A11", "1772071015_G12", "1772067058_D07", "1772067065_D01", "1772071015_A02", "1772071014_F01", "1772071015_D06", "1772071017_B02", "1772071017_D07", "1772071017_A11", "1772071017_B01", "1772071017_C07", "1772071015_H11", "1772071014_A05", "1772071017_A10", "1772071017_C08", "1772071017_B09", "1772067066_A09", "1772067065_A12", "1772071015_G04", "1772067066_B02", "1772071015_E06", "1772067064_E04", "1772071015_C01", "1772071014_F06", "1772071017_D10", "1772071017_C05", "1772071014_E05", "1772071017_E04", "1772058148_D08", "1772067065_F07", "1772062128_G08", "1772066102_B02", "1772063077_B03", "1772062114_H03", "1772066074_A03", "1772066102_C09", "1772062114_E02", "1772062115_A12", "1772062113_F08", "1772066108_B02", "1772066102_G06", "1772067059_E03", "1772071035_G04", "1772066102_C06", "1772067057_H02", "1772062115_G05", "1772066097_G03", "1772063064_G08", "1772067082_B01", "1772066099_C04", "1772071040_A12", "1772063078_F01", "1772067082_F03", "1772071044_A03", "1772067060_B04", "1772071045_C11", "1772067083_B10", "1772066077_E08", "1772063078_F12", "1772066099_C11", "1772063064_G03", "1772071036_E09", "1772062128_D11", "1772067058_A12", "1772063078_B02", "1772066108_E06", "1772066100_A12", "1772066073_B03", "1772067076_A06", "1772063061_H03", "1772066097_H05", "1772067065_A02", "1772066077_H12", "1772062128_G04", "1772062109_H03", "1772063063_F01", "1772062128_B10", "1772063061_B03", "1772063061_B05", "1772058177_G09", "1772066095_D02", "1772066097_G12", "1772066097_G02", "1772066100_G07", "1772066097_H01", "1772071045_H03", "1772067083_F08", "1772067083_H01", "1772066101_F04", "1772067058_H12", "1772067082_F02", "1772067058_H05", "1772071035_B09", "1772071015_H07", "1772071036_C02", "1772066108_F04", "1772071035_H02", "1772062109_H07", "1772067076_E03", "1772067059_G10", "1772067076_D04", "1772066099_H06", "1772066102_G12", "1772071035_E07", "1772066073_B02", "1772067076_A03", "1772066102_B11", "1772066089_A01", "1772066099_A01", "1772067057_H04", "1772066102_C11", "1772071045_A10", "1772066096_G01", "1772066102_H10", "1772066099_C12", "1772071044_H10", "1772067083_D10", "1772066099_E04", "1772066100_D08", "1772066089_H04", "1772066089_B06", "1772066102_G08", "1772066102_A04", "1772066097_B06", "1772067076_E04", "1772066097_C06", "1772067057_D12", "1772066100_A05", "1772071015_A11", "1772071015_C09", "1772062128_F10", "1772071017_H06", "1772071014_A12", "1772063077_H05" ], "rows": 3529, "table": true, "tojson": true }, { "name": "linnarsson_saver", "title": "SAVER recovered mouse brain single-cell RNA-seq dataset", "object": "linnarsson_saver", "class": [ "saver" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "SAVER-package", "title": "SAVER: Single-cell Analysis Via Expression Recovery", "topics": [ "SAVER-package" ] }, { "page": "optimize_variance", "title": "Optimizes variance", "topics": [ "calc.a", "calc.b", "calc.k" ] }, { "page": "calc_estimate", "title": "Calculate estimate", "topics": [ "calc.estimate", "calc.estimate.mean", "calc.estimate.null" ] }, { "page": "calc_loglik", "title": "Calculates marginal likelihood", "topics": [ "calc.loglik.a", "calc.loglik.b", "calc.loglik.k" ] }, { "page": "calc.maxcor", "title": "Calculate maximum correlation", "topics": [ "calc.maxcor" ] }, { "page": "calc.post", "title": "Calculates SAVER posterior", "topics": [ "calc.post" ] }, { "page": "combine.saver", "title": "Combines SAVER", "topics": [ "combine.saver" ] }, { "page": "cor_adjust", "title": "Calculates gene-to-gene and cell-to-cell SAVER correlation", "topics": [ "cor.cells", "cor.genes" ] }, { "page": "expr.predict", "title": "Calculates SAVER prediction.", "topics": [ "expr.predict" ] }, { "page": "get.mu", "title": "Output prior predictions", "topics": [ "get.mu" ] }, { "page": "linnarsson", "title": "Mouse brain single-cell RNA-seq dataset", "topics": [ "linnarsson" ] }, { "page": "linnarsson_saver", "title": "SAVER recovered mouse brain single-cell RNA-seq dataset", "topics": [ "linnarsson_saver" ] }, { "page": "sample.saver", "title": "Samples from SAVER", "topics": [ "sample.saver" ] }, { "page": "saver", "title": "Runs SAVER", "topics": [ "saver" ] }, { "page": "saver_fit", "title": "Fits SAVER", "topics": [ "saver.fit", "saver.fit.mean", "saver.fit.null" ] } ], "_readme": "https://github.com/mohuangx/saver/raw/HEAD/README.md", "_rundeps": [ "codetools", "doParallel", "foreach", "glmnet", "iterators", "lattice", "Matrix", "Rcpp", "RcppEigen", "shape", "survival" ], "_vignettes": [ { "source": "saver-tutorial.Rmd", "filename": "saver-tutorial.html", "title": "SAVER Tutorial", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Getting Started", "Preprocessing", "Running SAVER", "Using SAVER estimates", "Additional Settings", "Normalization", "Predicting certain genes", "Using other predictions", "Creating your own parallel backend", "Combining SAVER objects", "Sampling example", "Correlation example" ], "created": "2018-08-29 01:23:16", "modified": "2022-06-13 01:37:13", "commits": 6 } ], "_score": 8.968090505311157, "_indexed": true, "_nocasepkg": "saver", "_universes": [ "mohuangx" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.3", "date": "2026-07-03T14:20:02.000Z", "distro": "resolute", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/5de99b9d26965c471a5d88bfe4da6292db80e57942bf278e8710e62c2bb8a156", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" }, { "r": "4.6.1", "os": "linux", "version": "1.1.3", "date": "2026-07-03T14:19:51.000Z", "distro": "resolute", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/e8aa805ce1214139229543f4df4f7143b36eea456c4a11bd7cee09a45311fcb2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" }, { "r": "4.5.3", "os": "mac", "version": "1.1.3", "date": "2026-07-03T14:19:48.000Z", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/50037bc1ef9e65dc0e0d82788b64d0322889a3d30c8fa786eecd456ff24121c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" }, { "r": "4.6.1", "os": "mac", "version": "1.1.3", "date": "2026-07-03T14:20:19.000Z", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/91a9b02c3fb4382082a733063e71c4c227ae4709208f9f2346c08b9abeab6d30", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.3", "date": "2026-07-03T14:20:25.000Z", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/667409cad3cc9a8df5a388160ff99626b90e8574c75b92a052652242a957719a", "status": "success", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" }, { "r": "4.7.0", "os": "win", "version": "1.1.3", "date": "2026-07-03T14:19:07.000Z", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/9f0784fb36f9db108510155184d81205754ea323503cce3eb43913c12d93662a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" }, { "r": "4.5.3", "os": "win", "version": "1.1.3", "date": "2026-07-03T14:19:46.000Z", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/36bc552a030a0016fe31cb4d59c3359fa979dfd87acea13acf17ef4df2f3e57d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" }, { "r": "4.6.1", "os": "win", "version": "1.1.3", "date": "2026-07-03T14:19:03.000Z", "commit": "f28d719c1b77ce2ad03e4c066afd876eeade760f", "fileid": "https://r2.ropensci.org/485c6548f09d9817171ebf88be32caad85e6bd0b5c8f60d3e110d3c2b04488d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mohuangx/actions/runs/28666149613" } ] }