{ "_id": "6a1ee7f2b401979e734119b5", "Package": "gedi2", "Type": "Package", "Title": "Gene Expression Decomposition and Integration", "Version": "2.3.4", "Date": "2026-05-09", "Authors@R": "c(\nperson(\"Arsham\", \"Mikaeili Namini\", email = \"arsham.mikaeilinamini@mail.mcgill.ca\", role = c(\"aut\", \"cre\")),\nperson(\"Hamed\", \"S.Najafabadi\", email = \"hamed.najafabadi@mcgill.ca\", role = c(\"aut\"))\n)", "Description": "A memory-efficient implementation for integrating gene\nexpression data from single-cell RNA sequencing experiments.\nUses a C++ backend with thin R wrappers to enable analysis of\nlarge-scale single-cell datasets. The package supports multiple\ndata modalities including count matrices, paired data\n(splicing, RNA velocity, CITE-seq), and binary indicators. It\nimplements a latent variable model with block coordinate\ndescent optimization for dimensionality reduction and batch\neffect correction. Core algorithms are described in Madrigal et\nal. (2024) .", "License": "MIT + file LICENSE", "URL": "https://github.com/csglab/gedi2", "BugReports": "https://github.com/csglab/gedi2/issues", "Config/testthat/edition": "3", "SystemRequirements": "GNU make", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-19 11:17:29 UTC", "User": "root" }, "Author": "Arsham Mikaeili Namini [aut, cre], Hamed S.Najafabadi [aut]", "Maintainer": "Arsham Mikaeili Namini\n", "Config/pak/sysreqs": "make", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-05-19 08:41:47 UTC", "RemoteUrl": "https://github.com/cran/gedi2", "RemoteRef": "HEAD", "RemoteSha": "b9c69389c9da780d083e5ec2cae576b5a07c5283", "MD5sum": "15becfd19b8960bc0e83d800e7c263a6", "_user": "cran", "_type": "src", "_file": "gedi2_2.3.4.tar.gz", "_fileid": "c6509f1b91cc52beb0376d461ce83d023071c46fef57fed33da4732bda16c64a", "_filesize": 245117, "_sha256": "c6509f1b91cc52beb0376d461ce83d023071c46fef57fed33da4732bda16c64a", "_created": "2026-05-19T11:17:29.000Z", "_published": "2026-06-02T14:25:54.380Z", "_distro": "noble", "_jobs": [ { "job": 79093697689, "time": 270, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7082045005" }, { "job": 79093697238, "time": 272, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7082045444" }, { "job": 79093698951, "time": 266, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7082043492" }, { "job": 79093698651, "time": 299, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7082053700" }, { "job": 79093696271, "time": 323, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7081955160" }, { "job": 79093696468, "time": 207, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7360529552" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26093514790", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/gedi2", "_commit": { "id": "b9c69389c9da780d083e5ec2cae576b5a07c5283", "author": "Arsham Mikaeili Namini ", "committer": "cran-robot ", "message": "version 2.3.4\n", "time": 1779180107 }, "_maintainer": { "name": "Arsham Mikaeili Namini", "email": "arsham.mikaeilinamini@mail.mcgill.ca", "login": "arshammik", "description": "MSc Student of Human Genetics at CSG lab", "uuid": 92790984 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.0", "role": "Imports" }, { "package": "R6", "version": ">= 2.5.0", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.3.0", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "hdf5r", "role": "Suggests" }, { "package": "uwot", "role": "Suggests" }, { "package": "digest", "role": "Suggests" }, { "package": "glmnet", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "SeuratObject", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-21", "n": 1 } ], "_tags": [ { "name": "2.3.4", "date": "2026-05-19" } ], "_stars": 0, "_contributors": [ { "user": "arshammik", "count": 1, "uuid": 92790984 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gedi2" }, "_devurl": "https://github.com/csglab/gedi2", "_searchresults": 1, "_topics": [ "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gedi2.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "2.3.4", "date": "2026-05-19" } ], "_exports": [ "check_optional_dependencies", "CreateGEDIObject", "gedi_to_seurat", "install_optional_dependencies", "list_h5_structure", "plot_convergence", "plot_dispersion", "plot_embedding", "plot_feature_ratio", "plot_features", "plot_vector_field", "read_h5", "read_h5ad", "seurat_to_gedi", "write_h5ad" ], "_help": [ { "page": "check_optional_dependencies", "title": "Check GEDI Optional Dependencies", "topics": [ "check_optional_dependencies" ] }, { "page": "CreateGEDIObject", "title": "Create GEDI Object", "topics": [ "CreateGEDIObject" ] }, { "page": "gedi_to_seurat", "title": "Convert GEDI Model to Seurat Object", "topics": [ "gedi_to_seurat" ] }, { "page": "install_optional_dependencies", "title": "List Optional GEDI Dependencies", "topics": [ "install_optional_dependencies" ] }, { "page": "list_h5_structure", "title": "List structure of H5 or H5AD file", "topics": [ "list_h5_structure" ] }, { "page": "plot_convergence", "title": "Plot Training Convergence", "topics": [ "plot_convergence" ] }, { "page": "plot_dispersion", "title": "Plot Dispersion Analysis", "topics": [ "plot_dispersion" ] }, { "page": "plot_embedding", "title": "Plot Embedding with Improved API", "topics": [ "plot_embedding" ] }, { "page": "plot_feature_ratio", "title": "Plot Two-Feature Comparison", "topics": [ "plot_feature_ratio" ] }, { "page": "plot_features", "title": "Plot Multiple Features on Embedding", "topics": [ "plot_features" ] }, { "page": "plot_vector_field", "title": "Plot Vector Field from Dynamics Analysis", "topics": [ "plot_vector_field" ] }, { "page": "read_h5", "title": "Read 10X Genomics H5 file", "topics": [ "read_h5" ] }, { "page": "read_h5ad", "title": "Read H5AD file and convert to sparse matrix", "topics": [ "read_h5ad" ] }, { "page": "seurat_to_gedi", "title": "Convert Seurat Object to GEDI Model", "topics": [ "seurat_to_gedi" ] }, { "page": "write_h5ad", "title": "Write GEDI model to H5AD file", "topics": [ "write_h5ad" ] } ], "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_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" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_score": 1, "_indexed": true, "_nocasepkg": "gedi2", "_universes": [ "cran", "arshammik", "csglab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.3.4", "date": "2026-05-19T11:21:37.000Z", "distro": "noble", "arch": "aarch64", "commit": "b9c69389c9da780d083e5ec2cae576b5a07c5283", "fileid": "3ec7b666e55985af92643117bbe7543c0f35b817d660300a001e5f1af641e9fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26093514790" }, { "r": "4.7.0", "os": "linux", "version": "2.3.4", "date": "2026-05-19T11:21:24.000Z", "distro": "noble", "arch": "x86_64", "commit": "b9c69389c9da780d083e5ec2cae576b5a07c5283", "fileid": "f8ae8ca4f4f64957079e7e9f29f0692f438367015cb9a668a05008fb8764989c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26093514790" }, { "r": "4.6.0", "os": "linux", "version": "2.3.4", "date": "2026-05-19T11:21:26.000Z", "distro": "noble", "arch": "aarch64", "commit": "b9c69389c9da780d083e5ec2cae576b5a07c5283", "fileid": "391951174a2f2c6f810e1e823e32c300993c4ccd47dc46238b8dc9684c2565d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26093514790" }, { "r": "4.6.0", "os": "linux", "version": "2.3.4", "date": "2026-05-19T11:21:53.000Z", "distro": "noble", "arch": "x86_64", "commit": "b9c69389c9da780d083e5ec2cae576b5a07c5283", "fileid": "91efbdc51028d84f3adc0318d034253fa73de652d5397e79771de195dd7f8f3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26093514790" }, { "r": "4.6.0", "os": "wasm", "version": "2.3.4", "date": "2026-06-02T14:24:36.000Z", "arch": "emscripten", "commit": "b9c69389c9da780d083e5ec2cae576b5a07c5283", "fileid": "03911510545586d6be9c1ef5ed5dbb542f220493f0b7a950f3599cf143113e69", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26093514790" } ] }