{ "_id": "6a1b0a141d7bb097a0a0607c", "Package": "retrofit", "Title": "RETROFIT: Reference-free deconvolution of cell mixtures in\nspatial transcriptomics", "Version": "1.12.0", "Authors@R": "c(person(given = \"Adam\",\nfamily = \"Park\",\nrole = c(\"aut\",\"cre\"),\nemail = \"akp6031@psu.edu\",\ncomment = c()),\nperson(given = \"Roopali\",\nfamily = \"Singh\",\nrole = c(\"aut\"),\nemail = \"rus82@psu.edu\",\ncomment = c(ORCID = \"0000-0001-6539-6622\")),\nperson(given = \"Xiang\",\nfamily = \"Zhu\",\nrole = c(\"aut\"),\nemail = \"xiangzhu@psu.edu\",\ncomment = c(ORCID = \"0000-0003-1134-6413\")),\nperson(given = \"Qunhua\",\nfamily = \"Li\",\nrole = c(\"aut\"),\nemail = \"qunhua.li@psu.edu\",\ncomment = c(ORCID = \"0000-0003-0675-7648\"))\n)", "Description": "RETROFIT is a Bayesian non-negative matrix factorization\nframework to decompose cell type mixtures in ST data without\nusing external single-cell expression references. RETROFIT\noutperforms existing reference-based methods in estimating cell\ntype proportions and reconstructing gene expressions in\nsimulations with varying spot size and sample heterogeneity,\nirrespective of the quality or availability of the single-cell\nreference. RETROFIT recapitulates known cell-type localization\npatterns in a Slide-seq dataset of mouse cerebellum without\nusing any single-cell data.", "biocViews": "Transcriptomics, Visualization, RNASeq, Bayesian, Spatial,\nSoftware, GeneExpression, DimensionReduction,\nFeatureExtraction, SingleCell", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "FALSE", "URL": "https://github.com/qunhualilab/retrofit", "BugReports": "https://github.com/qunhualilab/retrofit/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:00:39 UTC", "RemoteUrl": "https://github.com/bioc/retrofit", "RemoteRef": "RELEASE_3_23", "RemoteSha": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 11:01:03 UTC", "User": "root" }, "Author": "Adam Park [aut, cre],\nRoopali Singh [aut] (ORCID: ),\nXiang Zhu [aut] (ORCID: ),\nQunhua Li [aut] (ORCID: )", "Maintainer": "Adam Park ", "MD5sum": "ffd65fecd15f61c4e54b7368f4297b89", "_user": "bioc-release", "_type": "src", "_file": "retrofit_1.12.0.tar.gz", "_fileid": "9c825c4722ad697b92e001137587e90d33977eb8df32d52d755cf63995b59ce0", "_filesize": 4596976, "_sha256": "9c825c4722ad697b92e001137587e90d33977eb8df32d52d755cf63995b59ce0", "_created": "2026-05-30T11:01:03.000Z", "_published": "2026-05-30T16:02:28.741Z", "_jobs": [ { "job": 78644306042, "time": 163, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307762911" }, { "job": 78644306061, "time": 295, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7307734129" }, { "job": 78644306066, "time": 202, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307766269" }, { "job": 78644306070, "time": 141, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307719691" }, { "job": 78644306063, "time": 199, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307765981" }, { "job": 78644306075, "time": 91, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309458990" }, { "job": 78644306073, "time": 221, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7307734510" }, { "job": 78644306081, "time": 141, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309464584" }, { "job": 78644306043, "time": 239, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307736572" }, { "job": 78643917654, "time": 228, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307703753" }, { "job": 78644306097, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307759799" }, { "job": 78644306106, "time": 129, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307760391" }, { "job": 78644306092, "time": 113, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307759043" }, { "job": 78644306099, "time": 114, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307759199" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/retrofit", "_commit": { "id": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381239 }, "_maintainer": { "name": "Adam Park", "email": "akp6031@psu.edu", "login": "akp6031", "description": "", "uuid": 90921267 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "Rcpp", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "DescTools", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "corrplot", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "colorspace", "role": "Suggests" }, { "package": "png", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "pals", "role": "Suggests" }, { "package": "RCurl", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.13.0", "bioc": "3.24" }, { "branch": "release", "version": "1.12.0", "bioc": "3.23" } ], "_topics": [ "transcriptomics", "visualization", "rnaseq", "bayesian", "spatial", "software", "geneexpression", "dimensionreduction", "featureextraction", "singlecell", "cpp" ], "_stars": 3, "_contributors": [ { "user": "akp6031", "count": 88, "uuid": 90921267 }, { "user": "roopali24", "count": 25, "uuid": 44040852 }, { "user": "xiangzhu", "count": 21, "uuid": 5986023 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 296, "source": "https://www.bioconductor.org/packages/stats/bioc/retrofit" }, "_devurl": "https://github.com/qunhualilab/retrofit", "_searchresults": 19, "_rbuild": "4.6.0", "_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/retrofit.html", "manual.pdf" ], "_homeurl": "https://github.com/qunhualilab/retrofit", "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotateWithCorrelations", "annotateWithMarkers", "decompose", "retrofit" ], "_datasets": [ { "name": "testSimulationData", "title": "simulation data", "object": "testSimulationData", "file": "testSimulationData.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "vignetteColonData", "title": "colon vignette", "object": "vignetteColonData", "file": "vignetteColonData.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "vignetteSimulationData", "title": "simulation vignette", "object": "vignetteSimulationData", "file": "vignetteSimulationData.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "annotateWithCorrelations", "title": "RETROFIT matching algorithm", "topics": [ "annotateWithCorrelations" ] }, { "page": "annotateWithMarkers", "title": "RETROFIT matching algorithm", "topics": [ "annotateWithMarkers" ] }, { "page": "decompose", "title": "RETROFIT decomposition algorithm", "topics": [ "decompose" ] }, { "page": "retrofit", "title": "RETROFIT", "topics": [ "retrofit" ] }, { "page": "testSimulationData", "title": "simulation data", "topics": [ "testSimulationData" ] }, { "page": "vignetteColonData", "title": "colon vignette", "topics": [ "vignetteColonData" ] }, { "page": "vignetteSimulationData", "title": "simulation vignette", "topics": [ "vignetteSimulationData" ] } ], "_readme": "https://github.com/bioc/retrofit/raw/RELEASE_3_23/README.md", "_rundeps": [ "Rcpp" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "ColonVignette.Rmd", "filename": "ColonVignette.html", "title": "Retrofit Colon Vignette", "author": "Adam Keebum Park, Roopali Singh", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Package Installation and other requirements", "Spatial Transcriptomics Data", "Reference-free Deconvolution", "Cell-type Annotation via annotated single-cell reference", "Cell-type Annotation via known marker genes", "Results and visualization", "Figure 4A: Proportion of different cell types in the tissue.", "Figure 4C: Localization of cell types with the dominant cell type in each spot", "Figure 4D: Gene expression of Epithelial marker genes across spots", "Figure 4E: Proportion of Epithelial cells across spots", "Figure 5A: Proportion of different cell types in different spots", "Figure 5D: Spots with 1 dominant cell type i.e., proportion > 0.5", "Figure 5E: Co-localized spots for Epithelial cells", "Figure 6C: Concordance between expression profiles of found genes obtained from RETROFIT and scRNA-seq data", "Session information" ], "created": "2022-12-24 12:33:59", "modified": "2023-02-27 01:32:25", "commits": 19 }, { "source": "SimulationVignette.Rmd", "filename": "SimulationVignette.html", "title": "Retrofit Simulation Vignette", "author": "Adam Keebum Park, Roopali Singh", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Package Installation", "Spatial Transcriptomics Data", "Deconvolution", "Cell-type Annotation", "Deconvolution and annotation in one step (Optional)", "Results", "Session information" ], "created": "2022-12-12 06:25:36", "modified": "2023-02-27 01:32:25", "commits": 17 } ], "_score": 5.357934847000454, "_indexed": false, "_nocasepkg": "retrofit", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/retrofit", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.12.0", "date": "2026-05-30T11:06:26.000Z", "distro": "noble", "arch": "aarch64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "4b2921ece56ddedd3f6b924e965f104a9621d18a6f567ae3297f35434208b9fe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.7.0", "os": "linux", "version": "1.12.0", "date": "2026-05-30T11:12:27.000Z", "distro": "noble", "arch": "x86_64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "1e540425bdf82744915ec0acb991c725e2963aec16061babfa1993dabfbcf0b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.6.0", "os": "linux", "version": "1.12.0", "date": "2026-05-30T11:03:54.000Z", "distro": "noble", "arch": "aarch64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "a3a916d783069d31046477e02abf6f5e1471d23f592c522c6ea2774451f95f99", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.6.0", "os": "linux", "version": "1.12.0", "date": "2026-05-30T11:12:27.000Z", "distro": "noble", "arch": "x86_64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "62aeb0bb4c9a16aa04e95a4ade45f42f1467a5e3aa17cde1672cbcfdb4bda324", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.5.3", "os": "mac", "version": "1.12.0", "date": "2026-05-30T16:00:56.000Z", "arch": "aarch64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "47a2571b403cb783d45740dcd37bbf6c5cb37b4044776eeb7aa6585178d44905", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.5.3", "os": "mac", "version": "1.12.0", "date": "2026-05-30T11:06:06.000Z", "arch": "x86_64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "8d0c7101c70f933d8a94267c7d40001f7ac70b5f7c31082785b9189847bb736f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.6.0", "os": "mac", "version": "1.12.0", "date": "2026-05-30T16:01:31.000Z", "arch": "aarch64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "d9c81dfe5b7d549147b6e007c55bb27afcbbf19a7abf5b5eedb2a9359b45b7ed", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.6.0", "os": "mac", "version": "1.12.0", "date": "2026-05-30T11:06:12.000Z", "arch": "x86_64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "439faf5d211a662dcaa9d9c85d90c466fcc53bc0c0d73cec903ec664df9ab38b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.6.0", "os": "wasm", "version": "1.12.0", "date": "2026-05-30T11:11:35.000Z", "arch": "emscripten", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "3fe76339c38ebe7d2de7be753294f23d3af4e5f9353d9281cda47900effc6a9f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.7.0", "os": "win", "version": "1.12.0", "date": "2026-05-30T11:10:52.000Z", "arch": "x86_64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "1a6c04bb429c122af69591eb93b2d144a79594920dcd335311c85ceffbde7171", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.5.3", "os": "win", "version": "1.12.0", "date": "2026-05-30T11:10:46.000Z", "arch": "x86_64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "b04257a739dadc32fd71d05340bc6ccac8fffa5096ed5ba6062429453752fe2a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" }, { "r": "4.6.0", "os": "win", "version": "1.12.0", "date": "2026-05-30T11:10:51.000Z", "arch": "x86_64", "commit": "16b8d80044622f7faec2a0fecdaaba7b6e6f1fc4", "fileid": "1603c241bbc0c0d222864598f5437d06f47b0dcc00794024e0dc7c2d031178ef", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681132541" } ] }