{ "_id": "6a212dfacd65a98ecbd2409b", "Package": "SiNMFiD", "Title": "Supervised iNMF informed Deconvolution", "Version": "0.0.0.9000", "Authors@R": "c(person(\"Joshua\", \"Sodicoff\", , \"sodicoff@uchicago.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Yichen\", \"Wang\", , \"wayichen@umich.edu\", role = \"ctb\"))", "Description": "A package for completing cell type deconvolution on bulk\nspatial transcriptomic data utilizing multiple reference\nscRNA-seq datasets.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "es", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nmake libhdf5-dev texlive libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev libssl-dev zlib1g-dev", "Repository": "https://welch-lab.r-universe.dev", "Date/Publication": "2024-03-15 15:24:47 UTC", "RemoteUrl": "https://github.com/welch-lab/SiNMFiD", "RemoteRef": "HEAD", "RemoteSha": "73012e2f3f981fdff6864896d9d68849f8929faf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 07:43:08 UTC", "User": "root" }, "Author": "Joshua Sodicoff [aut, cre],\nYichen Wang [ctb]", "Maintainer": "Joshua Sodicoff ", "MD5sum": "fe4a4970ab25bcc49bece0a3fec5eab3", "_user": "welch-lab", "_type": "src", "_file": "SiNMFiD_0.0.0.9000.tar.gz", "_fileid": "1544493a3d9d4368b61bab819be46e352f406bd2260cb8e1b5b7fa0f74e5a4de", "_filesize": 242041, "_sha256": "1544493a3d9d4368b61bab819be46e352f406bd2260cb8e1b5b7fa0f74e5a4de", "_created": "2026-06-04T07:43:08.000Z", "_published": "2026-06-04T07:49:14.667Z", "_distro": "noble", "_jobs": [ { "job": 79472735946, "time": 268, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7405857651" }, { "job": 79472735933, "time": 311, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7405871523" }, { "job": 79472735929, "time": 183, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7405830305" }, { "job": 79472735903, "time": 172, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7405826345" }, { "job": 79471964034, "time": 303, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7405768399" }, { "job": 79472735895, "time": 189, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7405832075" }, { "job": 79472735975, "time": 209, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7405838581" }, { "job": 79472735947, "time": 247, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7405851120" }, { "job": 79472735932, "time": 218, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7405841473" } ], "_buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/welch-lab/SiNMFiD", "_commit": { "id": "73012e2f3f981fdff6864896d9d68849f8929faf", "author": "Andrew Robbins ", "committer": "GitHub ", "message": "add missing dependency on lsa", "time": 1710516287 }, "_maintainer": { "name": "Joshua Sodicoff", "email": "sodicoff@uchicago.edu", "login": "jsodicoff", "description": "Genetics, Genomics, and Systems Biology Ph.D. student at the University of Chicago", "uuid": 44811472 }, "_registered": true, "_dependencies": [ { "package": "cowplot", "role": "Imports" }, { "package": "ggdendro", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "hdf5r", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "matrixTests", "role": "Imports" }, { "package": "rgl", "role": "Imports" }, { "package": "rliger", "role": "Imports" }, { "package": "transport", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "lsa", "role": "Imports" }, { "package": "cocoframer", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "welch-lab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "jsodicoff", "count": 44, "uuid": 44811472 }, { "user": "mvfki", "count": 5, "uuid": 28736557 }, { "user": "theaeon", "count": 1, "uuid": 9099529 } ], "_userbio": { "uuid": 45493916, "type": "organization", "name": "welch-lab" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SiNMFiD" }, "_devurl": "https://github.com/welch-lab/sinmfid", "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/SiNMFiD.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "analyze_gene_signatures", "analyze_spatial_correlation", "calculate_cell_sizes", "calculate_wasserstein", "cell_type_loading_histogram", "deconvolve_spatial", "generate_label_gifs", "generate_loading_gifs", "learn_gene_signatures", "load_objs", "mirror_spatial_coords", "overlay_subregion_gifs", "plot_analyze_gene_signatures", "plot_analyze_spatial_correlation", "plot_calculate_wasserstein", "plot_summarize_by_layer", "qc_spatial_data", "reference_3d_coordinates", "register_voxel_to_label", "sample_single_cell", "save_spatial_data", "select_defining_genes", "start_analysis", "subset_spatial_data", "summarize_by_layer", "summarize_clusters", "summarize_subregions", "transform_coords_to_ccf", "view_in_rgl", "voxelize_single_cells" ], "_help": [ { "page": "analyze_gene_signatures", "title": "Calculate relationships between cell types", "topics": [ "analyze_gene_signatures" ] }, { "page": "analyze_spatial_correlation", "title": "Calculate relationships between cell type distributions", "topics": [ "analyze_spatial_correlation" ] }, { "page": "calculate_cell_sizes", "title": "Calculate cell sizes with all reference data", "topics": [ "calculate_cell_sizes" ] }, { "page": "calculate_wasserstein", "title": "Calculate the Wasserstein distance between cell-types and genes", "topics": [ "calculate_wasserstein" ] }, { "page": "cell_type_loading_histogram", "title": "Generate histograms of loading by cell type", "topics": [ "cell_type_loading_histogram" ] }, { "page": "deconvolve_spatial", "title": "Title", "topics": [ "deconvolve_spatial" ] }, { "page": "generate_label_gifs", "title": "Title", "topics": [ "generate_label_gifs" ] }, { "page": "generate_loading_gifs", "title": "Generate gifs of cell type distributions derived from deconvolution in space", "topics": [ "generate_loading_gifs" ] }, { "page": "learn_gene_signatures", "title": "Title", "topics": [ "learn_gene_signatures" ] }, { "page": "load_objs", "title": "Load data from one of multiple formats", "topics": [ "load_objs" ] }, { "page": "mirror_spatial_coords", "title": "Flip axes in spatial data", "topics": [ "mirror_spatial_coords" ] }, { "page": "overlay_subregion_gifs", "title": "Title", "topics": [ "overlay_subregion_gifs" ] }, { "page": "plot_analyze_gene_signatures", "title": "Plot results of 'analyze_gene_signatures'", "topics": [ "plot_analyze_gene_signatures" ] }, { "page": "plot_analyze_spatial_correlation", "title": "Plot results of 'analyze_spatial_correlation'", "topics": [ "plot_analyze_spatial_correlation" ] }, { "page": "plot_calculate_wasserstein", "title": "Plot results of 'calculate_wasserstein'", "topics": [ "plot_calculate_wasserstein" ] }, { "page": "plot_summarize_by_layer", "title": "Plot results of 'summarize_by_layer'", "topics": [ "plot_summarize_by_layer" ] }, { "page": "qc_spatial_data", "title": "Quality-control spatial data", "topics": [ "qc_spatial_data" ] }, { "page": "reference_3d_coordinates", "title": "Generate silouhettes of the data along all three axes", "topics": [ "reference_3d_coordinates" ] }, { "page": "register_voxel_to_label", "title": "Transfer labels from coarse-grained sampled", "topics": [ "register_voxel_to_label" ] }, { "page": "sample_single_cell", "title": "Sample from single cell reference datasets", "topics": [ "sample_single_cell" ] }, { "page": "save_spatial_data", "title": "Add a new spatial dataset to the analysis directory", "topics": [ "save_spatial_data" ] }, { "page": "select_defining_genes", "title": "select variable genes with the Kruskal-Wallis test", "topics": [ "select_defining_genes" ] }, { "page": "start_analysis", "title": "Set up new analysis directory", "topics": [ "start_analysis" ] }, { "page": "subset_spatial_data", "title": "Subset a spatial dataset by coordinates for analysis", "topics": [ "subset_spatial_data" ] }, { "page": "summarize_by_layer", "title": "Summarize cell-type and gene expression data by", "topics": [ "summarize_by_layer" ] }, { "page": "summarize_clusters", "title": "Summarize cell types present in the source annotations", "topics": [ "summarize_clusters" ] }, { "page": "summarize_subregions", "title": "Summarize subregions of a vector of regions of interest", "topics": [ "summarize_subregions" ] }, { "page": "transform_coords_to_ccf", "title": "Use predefined transformations to match some modalities to the Allen CCF", "topics": [ "transform_coords_to_ccf" ] }, { "page": "view_in_rgl", "title": "Title", "topics": [ "view_in_rgl" ] }, { "page": "voxelize_single_cells", "title": "Coarse-grain spatial data to a predetermined resolution", "topics": [ "voxelize_single_cells" ] } ], "_readme": "https://github.com/welch-lab/SiNMFiD/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "base64enc", "BH", "BiocGenerics", "biocmake", "bit", "bit64", "bslib", "cachem", "checkmate", "cli", "cowplot", "cpp11", "data.table", "DelayedArray", "digest", "dir.expiry", "dplyr", "dqrng", "easy.utils", "evaluate", "farver", "fastmap", "fastmatch", "filelock", "FNN", "fontawesome", "fs", "generics", "ggdendro", "ggplot2", "ggrepel", "glue", "gridExtra", "gtable", "h5mread", "HDF5Array", "hdf5r", "hdf5r.Extra", "HighFive", "highr", "htmltools", "htmlwidgets", "igraph", "IRanges", "irlba", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "leidenAlg", "lifecycle", "lsa", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "matrixTests", "memoise", "mime", "patchwork", "pbmcapply", "pillar", "pkgconfig", "pROC", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppPlanc", "RcppProgress", "rgl", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "rliger", "rmarkdown", "RSpectra", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "sccore", "sitmo", "SnowballC", "SparseArray", "tibble", "tidyselect", "tinytex", "transport", "utf8", "uwot", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_score": 2, "_indexed": true, "_nocasepkg": "sinmfid", "_universes": [ "welch-lab", "jsodicoff" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.0.9000", "date": "2026-06-04T07:46:28.000Z", "distro": "noble", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "7a308c158e5a615ecf106053f2a0305df0badf6599603573456253ce75c0cf2c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" }, { "r": "4.6.0", "os": "linux", "version": "0.0.0.9000", "date": "2026-06-04T07:47:02.000Z", "distro": "noble", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "33044426a5dad14cb8918a428f63acbb171c0fa298cd8e446ba84ab7a5a23dbf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" }, { "r": "4.5.3", "os": "mac", "version": "0.0.0.9000", "date": "2026-06-04T07:45:22.000Z", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "0f5b7b1452616c0e74ff07266798a68e3c033064dc2126f29963268abd6bce02", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" }, { "r": "4.6.0", "os": "mac", "version": "0.0.0.9000", "date": "2026-06-04T07:45:20.000Z", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "c8456b814d5a4b35d13ffb869493cf4262c3b624be1fa748c52140518379b95d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.0.9000", "date": "2026-06-04T07:46:51.000Z", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "dec56ed0066907862eef71223bf6f404a117ecc172ea914c6f3fb97e90b2dbf7", "status": "success", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" }, { "r": "4.7.0", "os": "win", "version": "0.0.0.9000", "date": "2026-06-04T07:45:11.000Z", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "31d86bdeb63aef28f97f82a7fc7d460599b787c03090767c3c81d2fd8ca67714", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" }, { "r": "4.5.3", "os": "win", "version": "0.0.0.9000", "date": "2026-06-04T07:45:32.000Z", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "fe500ffa2b4926fe3cc8e8d42196a2d0c47e88015818e1e62d2f5b61f1d78cd2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" }, { "r": "4.6.0", "os": "win", "version": "0.0.0.9000", "date": "2026-06-04T07:45:22.000Z", "commit": "73012e2f3f981fdff6864896d9d68849f8929faf", "fileid": "8b2fe0e3636f40d2054e10f8848fa145f18d763c34b5cd0ec52d0b7aad521c65", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/26937885027" } ] }