{ "_id": "6a498d7e6d67900babdfae0e", "Package": "SIMLR", "Version": "1.39.0", "Date": "2026-03-09", "Title": "Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)", "Authors@R": "c(person(\"Daniele\", \"Ramazzotti\", role=c(\"aut\"),email=\"daniele.ramazzotti@unimib.it\",\ncomment = c(ORCID = \"0000-0002-6087-2666\")),\nperson(\"Bo\", \"Wang\", role=c(\"aut\"), email=\"wangbo.yunze@gmail.com\"),\nperson(\"Luca\", \"De Sano\", role=c(\"cre\",\"aut\"), email=\"luca.desano@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9618-3774\")),\nperson(\"Serafim\", \"Batzoglou\", role=c(\"ctb\")))", "Description": "Single-cell RNA-seq technologies enable high throughput\ngene expression measurement of individual cells, and allow the\ndiscovery of heterogeneity within cell populations. Measurement\nof cell-to-cell gene expression similarity is critical for the\nidentification, visualization and analysis of cell populations.\nHowever, single-cell data introduce challenges to conventional\nmeasures of gene expression similarity because of the high\nlevel of noise, outliers and dropouts. We develop a novel\nsimilarity-learning framework, SIMLR (Single-cell\nInterpretation via Multi-kernel LeaRning), which learns an\nappropriate distance metric from the data for dimension\nreduction, clustering and visualization.", "Encoding": "UTF-8", "License": "file LICENSE", "URL": "https://github.com/BatzoglouLabSU/SIMLR", "BugReports": "https://github.com/BatzoglouLabSU/SIMLR", "biocViews": "ImmunoOncology, Clustering, GeneExpression, Sequencing,\nSingleCell", "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:44:18 UTC", "RemoteUrl": "https://github.com/bioc/SIMLR", "RemoteRef": "HEAD", "RemoteSha": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "Packaged": { "Date": "2026-07-04 22:39:07 UTC", "User": "root" }, "Author": "Daniele Ramazzotti [aut] (ORCID:\n),\nBo Wang [aut],\nLuca De Sano [cre, aut] (ORCID:\n),\nSerafim Batzoglou [ctb]", "Maintainer": "Luca De Sano ", "_user": "bioc", "_type": "src", "_file": "SIMLR_1.39.0.tar.gz", "_fileid": "https://r2.ropensci.org/303f03f1a940ace9444e6a3d493c0023dca6c3865ebe2e73306d4332ce3f142a", "_filesize": 3833161, "_sha256": "303f03f1a940ace9444e6a3d493c0023dca6c3865ebe2e73306d4332ce3f142a", "_expires": "2026-10-12T22:47:23.000Z", "_created": "2026-07-04T22:39:07.000Z", "_published": "2026-07-04T22:47:26.143Z", "_bioccheck": { "error": 0, "warning": 2, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544", "_status": "success", "_upstream": "https://github.com/bioc/SIMLR", "_commit": { "id": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380258 }, "_maintainer": { "name": "Luca De Sano", "email": "luca.desano@gmail.com", "login": "luca-dex", "description": "", "uuid": 3315913, "orcid": "0000-0002-9618-3774" }, "_distro": "resolute", "_jobs": [ { "job": 85172866660, "time": 169, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8086080845" }, { "job": 85172866692, "time": 230, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8086088043" }, { "job": 85172866701, "time": 263, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8086091080" }, { "job": 85172866708, "time": 229, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8086087790" }, { "job": 85172866704, "time": 245, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8086089172" }, { "job": 85172866698, "time": 198, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8086084098" }, { "job": 85172866685, "time": 447, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8086110787" }, { "job": 85172866695, "time": 205, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8086084875" }, { "job": 85172866696, "time": 379, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8086103426" }, { "job": 85172629327, "time": 246, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8086061404" }, { "job": 85172866653, "time": 161, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8086079718" }, { "job": 85172866666, "time": 256, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8086090577" }, { "job": 85172866665, "time": 245, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8086089297" }, { "job": 85172866706, "time": 238, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8086088493" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "parallel", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "RcppAnnoy", "role": "Imports" }, { "package": "RSpectra", "role": "Imports" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-40", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.39.0", "bioc": "3.24" }, { "branch": "release", "version": "1.38.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "clustering", "geneexpression", "sequencing", "singlecell", "openblas", "cpp" ], "_stars": 115, "_contributors": [ { "user": "danro9685", "count": 196, "uuid": 5859159 }, { "user": "junjiezhujason", "count": 3, "uuid": 8904605 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 40, "_devurl": "https://github.com/batzogloulabsu/simlr", "_searchresults": 86, "_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/SIMLR.html", "LICENSE", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "SIMLR", "SIMLR_Estimate_Number_of_Clusters", "SIMLR_Feature_Ranking", "SIMLR_Large_Scale" ], "_datasets": [ { "name": "BuettnerFlorian", "title": "test dataset for SIMLR", "object": "BuettnerFlorian", "file": "BuettnerFlorian.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "ZeiselAmit", "title": "test dataset for SIMLR large scale", "object": "ZeiselAmit", "file": "ZeiselAmit.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "BuettnerFlorian", "title": "test dataset for SIMLR", "topics": [ "BuettnerFlorian" ] }, { "page": "SIMLR", "title": "SIMLR", "topics": [ "SIMLR" ] }, { "page": "SIMLR_Estimate_Number_of_Clusters", "title": "SIMLR Estimate Number of Clusters", "topics": [ "SIMLR_Estimate_Number_of_Clusters" ] }, { "page": "SIMLR_Feature_Ranking", "title": "SIMLR Feature Ranking", "topics": [ "SIMLR_Feature_Ranking" ] }, { "page": "SIMLR_Large_Scale", "title": "SIMLR Large Scale", "topics": [ "SIMLR_Large_Scale" ] }, { "page": "ZeiselAmit", "title": "test dataset for SIMLR large scale", "topics": [ "ZeiselAmit" ] } ], "_readme": "https://github.com/bioc/SIMLR/raw/HEAD/README.md", "_rundeps": [ "lattice", "Matrix", "pracma", "Rcpp", "RcppAnnoy", "RcppEigen", "RSpectra" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "v1_introduction.Rmd", "filename": "v1_introduction.html", "title": "Introduction", "author": "Daniele Ramazzotti, Bo Wang, Luca De Sano, Serafim Batzoglou", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Installing SIMLR", "Debug" ], "created": "2023-04-06 07:43:23", "modified": "2024-09-29 19:55:08", "commits": 4 }, { "source": "v2_running_SIMLR.Rmd", "filename": "v2_running_SIMLR.html", "title": "Running SIMLR", "author": "Daniele Ramazzotti, Bo Wang, Luca De Sano, Serafim Batzoglou", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-04-06 07:43:23", "modified": "2024-09-29 19:55:08", "commits": 2 } ], "_score": 8.59725628292514, "_indexed": true, "_nocasepkg": "simlr", "_universes": [ "bioc", "luca-dex", "batzogloulabsu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.39.0", "date": "2026-07-04T22:41:57.000Z", "distro": "resolute", "arch": "aarch64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/037e3b5fa17e0eb763243a5d17a972ace8c59a269a7f28bbbed0a4a44eb5f112", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.7.0", "os": "linux", "version": "1.39.0", "date": "2026-07-04T22:42:01.000Z", "distro": "resolute", "arch": "x86_64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/954fcb2a0965197956703028357d3912beba96ba27011c77ad5d40c9aded705d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.6.1", "os": "linux", "version": "1.39.0", "date": "2026-07-04T22:41:49.000Z", "distro": "resolute", "arch": "aarch64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/5c596b6e51895228092c6a8460af1aa80a1535da62dc74045d79ce475f67cdba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.6.1", "os": "linux", "version": "1.39.0", "date": "2026-07-04T22:41:49.000Z", "distro": "resolute", "arch": "x86_64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/e4f0fda075a8fbd443052576c9296878a959e17cf9d045ed3ec96cc5242c4898", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.5.3", "os": "mac", "version": "1.39.0", "date": "2026-07-04T22:40:54.000Z", "arch": "aarch64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/7b71115e1a50226d490c2388e9965393ac80c3928570d2fa311a92351ac49769", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.5.3", "os": "mac", "version": "1.39.0", "date": "2026-07-04T22:42:09.000Z", "arch": "x86_64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/92fbfb64561ebbbd4c6ef29c0e6d0c6b7ad4a1dbeb6a6a1ead0f5f65e7a7290e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.6.1", "os": "mac", "version": "1.39.0", "date": "2026-07-04T22:40:54.000Z", "arch": "aarch64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/ba6ad5cc2e8ae43194ddb1eada0002b1776c9d8965f5f7cb1cd90bd3eff3bf98", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.6.1", "os": "mac", "version": "1.39.0", "date": "2026-07-04T22:41:56.000Z", "arch": "x86_64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/df73045a519558f5e54037088f01fcec807052042061b9772741ab2b602ed918", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.6.0", "os": "wasm", "version": "1.39.0", "date": "2026-07-04T22:42:09.000Z", "arch": "emscripten", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/43be935aaa51a98a52711e5add0d50e77893345ceb21160f0828eb6705ec83d1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.7.0", "os": "win", "version": "1.39.0", "date": "2026-07-04T22:40:46.000Z", "arch": "x86_64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/d9daef56aa4e0beb5c73ff6d414d5e8568e503d758452c079b88340cf598beec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.5.3", "os": "win", "version": "1.39.0", "date": "2026-07-04T22:40:52.000Z", "arch": "x86_64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/b8abdd40046f9d619b36c9385db78da7c4aab73324ee6594803ff03529066a04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" }, { "r": "4.6.1", "os": "win", "version": "1.39.0", "date": "2026-07-04T22:40:32.000Z", "arch": "x86_64", "commit": "dd6fe994a67929d10433f2b53737d6dc1a3155ce", "fileid": "https://r2.ropensci.org/3497ef09c0fedbe1729fd25078055a136d55cb23b8654ae2e4a2b5cd92eb7b04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721835544" } ] }