{ "_id": "6ae2f6e995ca2370cc8ccf3f", "Package": "sctransform", "Type": "Package", "Title": "Variance Stabilizing Transformations for Single Cell UMI Data", "Version": "0.4.3", "Date": "2025-12-25", "Authors@R": "c(\nperson(given = \"Christoph\", family = \"Hafemeister\", email = \"christoph.hafemeister@nyu.edu\", role = \"aut\", comment = c(ORCID = \"0000-0001-6365-8254\")),\nperson(given = \"Saket\", family = \"Choudhary\", email = \"saketc@iitb.ac.in\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5202-7633\")),\nperson(given = \"Rahul\", family = \"Satija\", email = \"rsatija@nygenome.org\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9448-8833\"))\n)", "Description": "A normalization method for single-cell UMI count data\nusing a variance stabilizing transformation. The transformation\nis based on a negative binomial regression model with\nregularized parameters. As part of the same regression\nframework, this package also provides functions for batch\ncorrection, and data correction. See Hafemeister and Satija\n(2019) , and Choudhary and\nSatija (2022) for more\ndetails.", "URL": "https://github.com/satijalab/sctransform", "BugReports": "https://github.com/satijalab/sctransform/issues", "License": "GPL-3 | file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "SystemRequirements": "C++17", "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-28 08:34:02 UTC", "User": "root" }, "Author": "Christoph Hafemeister [aut] (ORCID:\n), Saket Choudhary [aut,\ncre] (ORCID: ), Rahul\nSatija [ctb] (ORCID: )", "Maintainer": "Saket Choudhary ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-01-10 08:45:16 UTC", "RemoteUrl": "https://github.com/cran/sctransform", "RemoteRef": "HEAD", "RemoteSha": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "_user": "cran", "_type": "src", "_file": "sctransform_0.4.3.tar.gz", "_fileid": "https://r2.ropensci.org/f70696bf762e428cb6cff173e112880f4b52fde5de808e345ebaed75b49d7776", "_filesize": 345735, "_sha256": "f70696bf762e428cb6cff173e112880f4b52fde5de808e345ebaed75b49d7776", "_expires": "2027-02-05T08:54:00.000Z", "_created": "2026-10-28T08:34:02.000Z", "_published": "2026-10-29T07:34:01.067Z", "_upstream": "https://github.com/cran/sctransform", "_status": "success", "_maintainer": { "name": "Saket Choudhary", "email": "saketc@iitb.ac.in", "login": "saketkc", "orcid": "0000-0001-5202-7633", "twitter": "@saketkc", "description": "", "uuid": 682153 }, "_jobs": [ { "job": 123319286447, "time": 170, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12802098724" }, { "job": 123319286491, "time": 513, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12803166059" }, { "job": 123319286342, "time": 136, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12802656184" }, { "job": 123319285897, "time": 931, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12802379291" }, { "job": 123319285030, "time": 235, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12803075023" }, { "job": 123319338992, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12802750952" }, { "job": 123319286121, "time": 230, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12802981495" }, { "job": 123319285795, "time": 210, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12802741405" }, { "job": 123319284248, "time": 249, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12880244592" }, { "job": 123319286485, "time": 1147, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12803248367" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150", "_commit": { "id": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "author": "Saket Choudhary ", "committer": "cran-robot ", "message": "version 0.4.3\n", "time": 1768034716 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.11.0", "role": "LinkingTo" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.5-0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "future.apply", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "parallelly", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "irlba", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "glmGamPoi", "role": "Enhances" } ], "_owner": "cran", "_selfowned": false, "_usedby": 117, "_updates": [ { "week": "2026-02", "n": 1 } ], "_tags": [ { "name": "0.4.3", "date": "2026-01-10" } ], "_stars": 1, "_contributors": [ { "user": "saketkc", "count": 2, "uuid": 682153 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 41177, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/sctransform" }, "_mentions": 34, "_devurl": "https://github.com/satijalab/sctransform", "_searchresults": 2, "_topics": [ "openblas", "cpp" ], "_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/sctransform.html", "LICENSE" ], "_homeurl": "https://github.com/satijalab/sctransform", "_realowner": "satijalab", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2018-11-18" }, { "version": "0.2.0", "date": "2019-04-12" }, { "version": "0.2.1", "date": "2019-12-17" }, { "version": "0.3", "date": "2020-09-20" }, { "version": "0.3.1", "date": "2020-10-08" }, { "version": "0.3.2", "date": "2020-12-16" }, { "version": "0.3.3", "date": "2022-01-13" }, { "version": "0.3.4", "date": "2022-08-20" }, { "version": "0.3.5", "date": "2022-09-21" }, { "version": "0.4.0", "date": "2023-09-19" }, { "version": "0.4.1", "date": "2023-10-19" }, { "version": "0.4.2", "date": "2025-04-30" }, { "version": "0.4.3", "date": "2026-01-10" } ], "_exports": [ "correct", "correct_counts", "diff_mean_test", "diff_mean_test_conserved", "generate", "get_model_var", "get_residual_var", "get_residuals", "plot_model", "plot_model_pars", "smooth_via_pca", "umify", "vst" ], "_datasets": [ { "name": "pbmc", "title": "Peripheral Blood Mononuclear Cells (PBMCs)", "object": "pbmc", "class": [ "dgCMatrix" ], "fields": [], "table": false, "tojson": false }, { "name": "umify_data", "title": "Transformation functions for umify", "object": "umify_data", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "clip_matrix_values", "title": "Clip matrix values to specified range", "topics": [ "clip_matrix_values" ] }, { "page": "close_progress_bar", "title": "Close progress bar", "topics": [ "close_progress_bar" ] }, { "page": "compare_expression", "title": "Compare gene expression between two groups", "topics": [ "compare_expression" ] }, { "page": "correct", "title": "Correct data by setting all latent factors to their median values and reversing the regression model", "topics": [ "correct" ] }, { "page": "correct_counts", "title": "Correct data by setting all latent factors to their median values and reversing the regression model", "topics": [ "correct_counts" ] }, { "page": "diff_mean_test", "title": "Non-parametric differential expression test for sparse non-negative data", "topics": [ "diff_mean_test" ] }, { "page": "diff_mean_test_conserved", "title": "Find differentially expressed genes that are conserved across samples", "topics": [ "diff_mean_test_conserved" ] }, { "page": "generate", "title": "Generate data from regularized models.", "topics": [ "generate" ] }, { "page": "get_model_formula", "title": "Extract model formula from model string", "topics": [ "get_model_formula" ] }, { "page": "get_model_var", "title": "Return average variance under negative binomial model", "topics": [ "get_model_var" ] }, { "page": "get_nz_median2", "title": "Get median of non zero UMIs from a count matrix", "topics": [ "get_nz_median2" ] }, { "page": "get_residual_var", "title": "Return variance of residuals of regularized models", "topics": [ "get_residual_var" ] }, { "page": "get_residuals", "title": "Return Pearson or deviance residuals of regularized models", "topics": [ "get_residuals" ] }, { "page": "is_outlier", "title": "Identify outliers", "topics": [ "is_outlier" ] }, { "page": "make.sparse", "title": "Convert a given matrix to dgCMatrix", "topics": [ "make.sparse" ] }, { "page": "pbmc", "title": "Peripheral Blood Mononuclear Cells (PBMCs)", "topics": [ "pbmc" ] }, { "page": "plot_model", "title": "Plot observed UMI counts and model", "topics": [ "plot_model" ] }, { "page": "plot_model_pars", "title": "Plot estimated and fitted model parameters", "topics": [ "plot_model_pars" ] }, { "page": "prepare_regressor_data", "title": "Prepare regressor data from vst object and cell attributes", "topics": [ "prepare_regressor_data" ] }, { "page": "robust_scale", "title": "Robust scale using median and mad", "topics": [ "robust_scale" ] }, { "page": "robust_scale_binned", "title": "Robust scale using median and mad per bin", "topics": [ "robust_scale_binned" ] }, { "page": "row_gmean", "title": "Geometric mean per row", "topics": [ "row_gmean" ] }, { "page": "row_var", "title": "Variance per row", "topics": [ "row_var" ] }, { "page": "setup_progress_bar", "title": "Setup progress bar for batch processing", "topics": [ "setup_progress_bar" ] }, { "page": "smooth_via_pca", "title": "Smooth data by PCA", "topics": [ "smooth_via_pca" ] }, { "page": "umify", "title": "Quantile normalization of cell-level data to match typical UMI count data", "topics": [ "umify" ] }, { "page": "umify_data", "title": "Transformation functions for umify", "topics": [ "umify_data" ] }, { "page": "update_progress_bar", "title": "Update progress bar", "topics": [ "update_progress_bar" ] }, { "page": "vst", "title": "Variance stabilizing transformation for UMI count data", "topics": [ "vst" ] } ], "_readme": "https://github.com/cran/sctransform/raw/HEAD/README.md", "_rundeps": [ "cli", "codetools", "cpp11", "digest", "dplyr", "farver", "future", "future.apply", "generics", "ggplot2", "globals", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "MASS", "Matrix", "matrixStats", "parallelly", "pillar", "pkgconfig", "plyr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "liblapack", "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": "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" } ], "_score": 6.858931823188126, "_indexed": false, "_nocasepkg": "sctransform", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.3", "date": "2026-10-28T08:36:36.000Z", "distro": "resolute", "arch": "aarch64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/902a3bc1e575cb92ae59b204241ff5d5fd1d803b9735a7ca3b9fc2c799a0f3d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.7.0", "os": "linux", "version": "0.4.3", "date": "2026-10-28T08:41:55.000Z", "distro": "resolute", "arch": "x86_64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/1734d56d8e9983efff7ad5cb6dbad21acc623fbcfe72363786b7b969bb7d02b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.6.1", "os": "linux", "version": "0.4.3", "date": "2026-10-28T08:36:03.000Z", "distro": "resolute", "arch": "aarch64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/840e210b2850509c088988a2ae43b2aa6cdf444d49210f0023dbe81a17593797", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.6.1", "os": "linux", "version": "0.4.3", "date": "2026-10-28T08:45:44.000Z", "distro": "resolute", "arch": "x86_64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/81cf993ef28462d23b79acf47a7d408b3038e62d7cd5641ece4cd5f3bf1e641e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.3", "date": "2026-10-28T08:36:15.000Z", "arch": "emscripten", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/d53f1610ebb574ed429cbb0b7b0b56f889c1ecbd5cac95b4a6f29d2865cbe3d7", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.7.0", "os": "win", "version": "0.4.3", "date": "2026-10-28T08:37:13.000Z", "arch": "aarch64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/ef2b68818846e10ea9123b11973387858729b27674e8e68c45ec6605d06e4d73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.7.0", "os": "win", "version": "0.4.3", "date": "2026-10-28T08:36:06.000Z", "arch": "x86_64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/46d8990a189c328673bc755730d97f22a5ae0c311c2f4206bd24275f8f37ade0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.6.1", "os": "win", "version": "0.4.3", "date": "2026-10-29T07:30:15.000Z", "arch": "aarch64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/f3c4bf65db154e5dd6afff3e7446626e007e4548561298c76672ea35aff8c41f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" }, { "r": "4.6.1", "os": "win", "version": "0.4.3", "date": "2026-10-28T08:49:55.000Z", "arch": "x86_64", "commit": "18ab33de11b98a0f857df234c0ac7eb347cad3db", "fileid": "https://r2.ropensci.org/c1c7337e327e62ff16d808beebd6e5c4d813d91db97d3d486c58376c8f8c83dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40657244150" } ] }