{ "_id": "6a1fd323b401979e73435c40", "Package": "monocle3", "Title": "Clustering, Differential Expression, and Trajectory Analysis for\nSingle-Cell RNA-Seq", "Version": "1.4.27", "Authors@R": "c(\nperson(given = \"Hannah\",\nfamily = \"Pliner\",\nrole = c(\"aut\"),\nemail = \"hpliner@uw.edu\"),\nperson(given = \"Xiaojie\",\nfamily = \"Qiu\",\nrole = c(\"aut\"),\nemail = \"xqiu@uw.edu\"),\nperson(given = \"Cole\",\nfamily = \"Trapnell\",\nrole = c(\"aut\"),\nemail = \"coletrap@uw.edu\"),\nperson(given = \"Brent\",\nfamily = \"Ewing\",\nrole = c(\"cre\"),\nemail = \"bge@uw.edu\"))", "Description": "Monocle 3 performs clustering, differential expression and\ntrajectory analysis for single-cell expression experiments. It\norders individual cells according to progress through a\nbiological process, without knowing ahead of time which genes\ndefine progress through that process. Monocle 3 also performs\ndifferential expression analysis, clustering, visualization,\nand other useful tasks on single-cell expression data. It is\ndesigned to work with RNA-Seq data, but could be used with\nother types as well.", "biocViews": "Software, SingleCell, RNASeq, ATACSeq, Normalization,\nPreprocessing, DimensionReduction, Visualization,\nQualityControl, Clustering, Classification, Annotation,\nGeneExpression, DifferentialExpression", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Remotes": [ "github::bnprks/BPCells/r", "github::cole-trapnell-lab/speedglm" ], "VignetteBuilder": "knitr", "Language": "en-US", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-03 06:48:31 UTC", "User": "root" }, "Maintainer": "Brent Ewing ", "Config/pak/sysreqs": "libabsl-dev libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev libglpk-dev make libharfbuzz-dev libicu-dev\nlibjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev libx11-dev zlib1g-dev", "Repository": "https://blaserlab.r-universe.dev", "Date/Publication": "2026-05-04 22:44:38 UTC", "RemoteUrl": "https://github.com/cole-trapnell-lab/monocle3", "RemoteRef": "HEAD", "RemoteSha": "536f1033d6de7c957f26a1f403f81efbd825e0db", "Author": "Hannah Pliner [aut],\nXiaojie Qiu [aut],\nCole Trapnell [aut],\nBrent Ewing [cre]", "MD5sum": "c7c63ea235f618358f2684afe823068e", "_user": "blaserlab", "_type": "src", "_file": "monocle3_1.4.27.tar.gz", "_fileid": "80ac3aa48d5b1ed00a7c1af345974da8686e92c1fa0a5c44db5b2614e8e156f0", "_filesize": 4348173, "_sha256": "80ac3aa48d5b1ed00a7c1af345974da8686e92c1fa0a5c44db5b2614e8e156f0", "_created": "2026-06-03T06:48:31.000Z", "_published": "2026-06-03T07:09:23.916Z", "_distro": "noble", "_jobs": [ { "job": 79237859337, "time": 698, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7377801094" }, { "job": 79237859321, "time": 891, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7377854901" }, { "job": 79237859315, "time": 693, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7377799688" }, { "job": 79237859390, "time": 789, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7377826622" }, { "job": 79237859392, "time": 484, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7377738958" }, { "job": 79237859383, "time": 848, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7377843497" }, { "job": 79237859407, "time": 951, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7377871817" }, { "job": 79237859426, "time": 1183, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7377936081" }, { "job": 79237156439, "time": 304, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7377604079" }, { "job": 79237859263, "time": 217, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7377664738" }, { "job": 79237859319, "time": 616, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7377777231" }, { "job": 79237859354, "time": 939, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7377868807" }, { "job": 79237859332, "time": 919, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7377863213" } ], "_buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cole-trapnell-lab/monocle3", "_commit": { "id": "536f1033d6de7c957f26a1f403f81efbd825e0db", "author": "brgew ", "committer": "GitHub ", "message": "Merge pull request #783 from cole-trapnell-lab/bge.grr_fix.20260504\n\nFix archived grr dependency.", "time": 1777934678 }, "_maintainer": { "name": "Brent Ewing", "email": "bge@uw.edu", "login": "brgew", "description": "\n", "uuid": 11478979 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "SingleCellExperiment", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "assertthat", "version": ">= 0.2.1", "role": "Imports" }, { "package": "batchelor", "role": "Imports" }, { "package": "BiocGenerics", "version": ">= 0.28.0", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "BPCells", "role": "Imports" }, { "package": "DelayedArray", "version": ">= 0.8.0", "role": "Imports" }, { "package": "DelayedMatrixStats", "version": ">= 1.4.0", "role": "Imports" }, { "package": "digest", "version": ">= 0.6.28", "role": "Imports" }, { "package": "dplyr", "version": ">= 0.8.0.1", "role": "Imports" }, { "package": "future", "version": ">= 1.23.0", "role": "Imports" }, { "package": "ggdist", "version": ">= 3.3.0", "role": "Imports" }, { "package": "ggforce", "version": ">= 0.4.1", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.1.1", "role": "Imports" }, { "package": "ggrastr", "role": "Imports" }, { "package": "ggrepel", "version": ">= 0.8.1", "role": "Imports" }, { "package": "HDF5Array", "role": "Imports" }, { "package": "igraph", "version": ">= 1.5.0", "role": "Imports" }, { "package": "irlba", "version": ">= 2.3.3", "role": "Imports" }, { "package": "leidenbase", "version": ">= 0.1.25", "role": "Imports" }, { "package": "limma", "version": ">= 3.38.3", "role": "Imports" }, { "package": "lme4", "version": ">= 1.1-27", "role": "Imports" }, { "package": "lmtest", "version": ">= 0.9-36", "role": "Imports" }, { "package": "MASS", "version": ">= 7.3-51.4", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.2-17", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "openssl", "role": "Imports" }, { "package": "pbapply", "version": ">= 1.4-0", "role": "Imports" }, { "package": "pbmcapply", "version": ">= 1.4.1", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "plotly", "version": ">= 4.9.0", "role": "Imports" }, { "package": "plyr", "version": ">= 1.8.4", "role": "Imports" }, { "package": "proxy", "version": ">= 0.4-23", "role": "Imports" }, { "package": "pscl", "version": ">= 1.5.2", "role": "Imports" }, { "package": "purrr", "version": ">= 0.3.2", "role": "Imports" }, { "package": "RANN", "version": ">= 2.6.1", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.1", "role": "Imports" }, { "package": "reshape2", "version": ">= 1.4.3", "role": "Imports" }, { "package": "rsample", "version": ">= 0.0.5", "role": "Imports" }, { "package": "RhpcBLASctl", "role": "Imports" }, { "package": "RcppAnnoy", "role": "Imports" }, { "package": "RcppHNSW", "version": ">= 0.3.0", "role": "Imports" }, { "package": "Rtsne", "version": ">= 0.15", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "slam", "version": ">= 0.1-45", "role": "Imports" }, { "package": "spdep", "version": ">= 1.1-2", "role": "Imports" }, { "package": "speedglm", "version": ">= 0.3-2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "version": ">= 1.4.0", "role": "Imports" }, { "package": "SummarizedExperiment", "version": ">= 1.11.5", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "uwot", "version": ">= 0.1.8", "role": "Imports" }, { "package": "tibble", "version": ">= 2.1.1", "role": "Imports" }, { "package": "tidyr", "version": ">= 0.8.3", "role": "Imports" }, { "package": "viridis", "version": ">= 0.5.1", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "pryr", "version": ">= 0.1.4", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "scran", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" } ], "_owner": "cole-trapnell-lab", "_selfowned": false, "_usedby": 2, "_updates": [ { "week": "2025-23", "n": 2 }, { "week": "2026-19", "n": 1 } ], "_tags": [ { "name": "v1.4.26", "date": "2025-06-05" }, { "name": "v1.4.27", "date": "2026-05-04" } ], "_topics": [ "software", "singlecell", "rnaseq", "atacseq", "normalization", "preprocessing", "dimensionreduction", "visualization", "qualitycontrol", "clustering", "classification", "annotation", "geneexpression", "differentialexpression", "single-cell-rna-seq", "cpp" ], "_stars": 453, "_contributors": [ { "user": "brgew", "count": 502, "uuid": 11478979 }, { "user": "hpliner", "count": 319, "uuid": 7491799 }, { "user": "ctrapnell", "count": 227, "uuid": 294681 }, { "user": "rfriedman22", "count": 10, "uuid": 14191132 }, { "user": "jenniferfranks", "count": 6, "uuid": 18276218 }, { "user": "maddyduran", "count": 1, "uuid": 17054655 }, { "user": "mjsteinbaugh", "count": 1, "uuid": 1760218 }, { "user": "zhangguy", "count": 1, "uuid": 10910559 } ], "_userbio": { "uuid": 62366303, "type": "user", "name": "Brad Blaser", "description": "Experimental Hematologist and Fish Fancier" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/monocle3" }, "_devurl": "https://github.com/cole-trapnell-lab/monocle3", "_searchresults": 3248, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/monocle3.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "aggregate_gene_expression", "align_cds", "align_transform", "choose_cells", "choose_graph_segments", "clear_cds_slots", "cluster_cells", "clusters", "coefficient_table", "combine_cds", "compare_models", "convert_counts_matrix", "counts_row_order", "counts<-", "detect_genes", "estimate_size_factors", "evaluate_fits", "exprs", "fData", "fData<-", "find_gene_modules", "fit_models", "fix_missing_cell_labels", "generate_garnett_marker_file", "get_citations", "graph_test", "identity_table", "learn_graph", "load_a549", "load_cellranger_data", "load_mm_data", "load_monocle_objects", "load_mtx_data", "load_transform_models", "load_worm_embryo", "load_worm_l2", "make_cds_nn_index", "make_nn_index", "model_predictions", "new_cell_data_set", "normalized_counts", "order_cells", "partitions", "pData", "pData<-", "plot_cells", "plot_cells_3d", "plot_cells_per_sample_and_perturbation", "plot_genes_by_group", "plot_genes_hybrid", "plot_genes_in_pseudotime", "plot_genes_violin", "plot_mito_umi_per_cell", "plot_pc_variance_explained", "plot_percent_cells_positive", "plot_umi_per_cell", "plot_umi_per_cell_and_perturbation", "preprocess_cds", "preprocess_transform", "principal_graph", "principal_graph_aux", "principal_graph_aux<-", "principal_graph<-", "pseudotime", "reduce_dimension", "reduce_dimension_transform", "save_monocle_objects", "save_transform_models", "search_cds_nn_index", "search_nn_index", "search_nn_matrix", "set_cds_nn_index", "set_cds_row_order_matrix", "set_matrix_control", "size_factors", "top_markers", "transfer_cell_labels" ], "_help": [ { "page": "aggregate_gene_expression", "title": "Creates a matrix with aggregated expression values for arbitrary groups of genes", "topics": [ "aggregate_gene_expression" ] }, { "page": "align_cds", "title": "Align cells from different groups within a cds", "topics": [ "align_cds" ] }, { "page": "align_transform", "title": "Apply an alignment transform model to a cell_data_set.", "topics": [ "align_transform" ] }, { "page": "bpcells_prcomp_irlba", "title": "Principal Components Analysis on BPCells IterableMatrix", "topics": [ "bpcells_prcomp_irlba" ] }, { "page": "calc_principal_graph", "title": "Function to automatically learn the structure of data by either using L1-graph or the spanning-tree formulization", "topics": [ "calc_principal_graph" ] }, { "page": "cell_data_set", "title": "The cell_data_set class", "topics": [ "cell_data_set", "cell_data_set-class" ] }, { "page": "cell_data_set-methods", "title": "Methods for the cell_data_set class", "topics": [ "cell_data_set-methods" ] }, { "page": "choose_cells", "title": "Choose cells interactively to subset a cds", "topics": [ "choose_cells" ] }, { "page": "choose_graph_segments", "title": "Choose cells along the path of a principal graph", "topics": [ "choose_graph_segments" ] }, { "page": "clear_cds_slots", "title": "Clear CDS slots", "topics": [ "clear_cds_slots" ] }, { "page": "cluster_cells", "title": "Cluster cells using Louvain/Leiden community detection", "topics": [ "cluster_cells" ] }, { "page": "clusters", "title": "Generic to extract clusters from CDS object", "topics": [ "clusters" ] }, { "page": "clusters-cell_data_set-method", "title": "Method to extract clusters from CDS object", "topics": [ "clusters,cell_data_set-method" ] }, { "page": "coefficient_table", "title": "Extract coefficient table from a fit_models result.", "topics": [ "coefficient_table" ] }, { "page": "combine_cds", "title": "Combine a list of cell_data_set objects", "topics": [ "combine_cds" ] }, { "page": "compare_models", "title": "Compare goodness of fit of two models.", "topics": [ "compare_models" ] }, { "page": "convert_counts_matrix", "title": "Convert the counts matrix class in the given CDS.", "topics": [ "convert_counts_matrix" ] }, { "page": "counts_row_order", "title": "Generic to access cds row order BPCells counts matrix.", "topics": [ "counts_row_order" ] }, { "page": "counts_row_order-cell_data_set-method", "title": "Method to access cds row order BPCells counts matrix", "topics": [ "counts_row_order,cell_data_set-method" ] }, { "page": "detect_genes", "title": "Detects genes above minimum threshold.", "topics": [ "detect_genes" ] }, { "page": "estimate_size_factors", "title": "Function to calculate size factors for single-cell RNA-seq data", "topics": [ "estimate_size_factors" ] }, { "page": "evaluate_fits", "title": "Evaluate fit of model objects.", "topics": [ "evaluate_fits" ] }, { "page": "exprs", "title": "Generic to access cds count matrix", "topics": [ "exprs" ] }, { "page": "exprs-cell_data_set-method", "title": "Method to access cds count matrix", "topics": [ "exprs,cell_data_set-method" ] }, { "page": "fData", "title": "Generic to access cds rowData table", "topics": [ "fData" ] }, { "page": "fData-cell_data_set-method", "title": "Method to access cds rowData table", "topics": [ "fData,cell_data_set-method" ] }, { "page": "fData-set", "title": "Generic to set cds rowData table", "topics": [ "fData<-" ] }, { "page": "fData-set-cell_data_set-method", "title": "Method to set cds rowData table", "topics": [ "fData<-,cell_data_set-method" ] }, { "page": "find_gene_modules", "title": "Cluster genes into modules that are co-expressed across cells.", "topics": [ "find_gene_modules" ] }, { "page": "fit_models", "title": "Fits a model for each gene in a cell_data_set object.", "topics": [ "fit_models" ] }, { "page": "fix_missing_cell_labels", "title": "Replace NA cell column data values left after running transfer_cell_labels.", "topics": [ "fix_missing_cell_labels" ] }, { "page": "generate_centers", "title": "Function to reproduce the behavior of eye function in matlab", "topics": [ "generate_centers" ] }, { "page": "generate_garnett_marker_file", "title": "Generate a Garnett marker file from top_markers output.", "topics": [ "generate_garnett_marker_file" ] }, { "page": "get_citations", "title": "Access citations for methods used during analysis.", "topics": [ "get_citations" ] }, { "page": "get_genome_in_matrix_path", "title": "Get a genome from Cell Ranger output", "topics": [ "get_genome_in_matrix_path" ] }, { "page": "graph_test", "title": "Test genes for differential expression based on the low dimensional embedding and the principal graph", "topics": [ "graph_test" ] }, { "page": "identity_table", "title": "Report matrix and model identity information.", "topics": [ "identity_table" ] }, { "page": "learn_graph", "title": "Learn principal graph from the reduced dimension space using reversed graph embedding", "topics": [ "learn_graph" ] }, { "page": "load_a549", "title": "Build a small cell_data_set.", "topics": [ "load_a549" ] }, { "page": "load_cellranger_data", "title": "Load data from the 10x Genomics Cell Ranger pipeline", "topics": [ "load_cellranger_data" ] }, { "page": "load_mm_data", "title": "Load data from matrix market format files.", "topics": [ "load_mm_data" ] }, { "page": "load_monocle_objects", "title": "Load a full Monocle3 cell_data_set.", "topics": [ "load_monocle_objects" ] }, { "page": "load_mtx_data", "title": "Load data from matrix market format", "topics": [ "load_mtx_data" ] }, { "page": "load_transform_models", "title": "Load transform models into a cell_data_set.", "topics": [ "load_transform_models" ] }, { "page": "load_worm_embryo", "title": "Build a cell_data_set from C. elegans embryo data.", "topics": [ "load_worm_embryo" ] }, { "page": "load_worm_l2", "title": "Build a cell_data_set from C. elegans L2 data.", "topics": [ "load_worm_l2" ] }, { "page": "make_cds_nn_index", "title": "Make and store a nearest neighbor index in the cell_data_set.", "topics": [ "make_cds_nn_index" ] }, { "page": "make_nn_index", "title": "Make a nearest neighbor index.", "topics": [ "make_nn_index" ] }, { "page": "mc_es_apply", "title": "Multicore apply-like function for cell_data_set", "topics": [ "mc_es_apply" ] }, { "page": "model_predictions", "title": "Predict values of new data using fit_models model.", "topics": [ "model_predictions" ] }, { "page": "new_cell_data_set", "title": "Create a new cell_data_set object.", "topics": [ "new_cell_data_set" ] }, { "page": "normalized_counts", "title": "Return a size-factor normalized and (optionally) log-transformed expression matrix", "topics": [ "normalized_counts" ] }, { "page": "order_cells", "title": "Orders cells according to pseudotime.", "topics": [ "order_cells" ] }, { "page": "partitions", "title": "Generic to extract partitions from CDS object", "topics": [ "partitions" ] }, { "page": "partitions-cell_data_set-method", "title": "Method to extract partitions from CDS object", "topics": [ "partitions,cell_data_set-method" ] }, { "page": "pData", "title": "Generic to access cds colData table", "topics": [ "pData" ] }, { "page": "pData-cell_data_set-method", "title": "Method to access cds colData table", "topics": [ "pData,cell_data_set-method" ] }, { "page": "pData-set", "title": "Generic to set cds colData table", "topics": [ "pData<-" ] }, { "page": "pData-set-cell_data_set-method", "title": "Method to set cds colData table", "topics": [ "pData<-,cell_data_set-method" ] }, { "page": "plot_cells", "title": "Plots the cells along with their trajectories.", "topics": [ "plot_cells" ] }, { "page": "plot_cells_3d", "title": "Plot a dataset and trajectory in 3 dimensions", "topics": [ "plot_cells_3d" ] }, { "page": "plot_cells_per_sample_and_perturbation", "title": "Make a boxplot of the number of cells per sample, with each perturbation as a separate box. Optionally facet by a second value.", "topics": [ "plot_cells_per_sample_and_perturbation" ] }, { "page": "plot_genes_by_group", "title": "Create a dot plot to visualize the mean gene expression and percentage of expressed cells in each group of cells", "topics": [ "plot_genes_by_group" ] }, { "page": "plot_genes_hybrid", "title": "Plot expression for one or more genes as a hybrid histogram-interval with a Sina plot overlay.", "topics": [ "plot_genes_hybrid" ] }, { "page": "plot_genes_in_pseudotime", "title": "Plots expression for one or more genes as a function of pseudotime", "topics": [ "plot_genes_in_pseudotime" ] }, { "page": "plot_genes_violin", "title": "Plot expression for one or more genes as a violin plot", "topics": [ "plot_genes_violin" ] }, { "page": "plot_mito_umi_per_cell", "title": "Plot a histogram of the percentage of UMIs mapping to mitochondria for each cell.", "topics": [ "plot_mito_umi_per_cell" ] }, { "page": "plot_pc_variance_explained", "title": "Plots the fraction of variance explained by the each component based on PCA from the normalized expression data determined using preprocess_cds. This is the fraction of the component variance relative to the variance of the components retained in the PCA; not the total variance.", "topics": [ "plot_pc_variance_explained" ] }, { "page": "plot_percent_cells_positive", "title": "Plots the number of cells expressing one or more genes above a given value as a barplot", "topics": [ "plot_percent_cells_positive" ] }, { "page": "plot_umi_per_cell", "title": "Plot a histogram of the number of UMIs per cell with an optional vertical line showing the cutoff for outliers.", "topics": [ "plot_umi_per_cell" ] }, { "page": "plot_umi_per_cell_and_perturbation", "title": "Make a boxplot of the number of UMIs per cell, with each perturbation as a separate box. Optionally facet by a second value.", "topics": [ "plot_umi_per_cell_and_perturbation" ] }, { "page": "preprocess_cds", "title": "Preprocess a cds to prepare for trajectory inference", "topics": [ "preprocess_cds" ] }, { "page": "preprocess_transform", "title": "Apply a preprocess transform model to a cell_data_set.", "topics": [ "preprocess_transform" ] }, { "page": "principal_graph", "title": "Generic to extract principal graph from CDS", "topics": [ "principal_graph" ] }, { "page": "principal_graph_aux", "title": "Generic to extract principal graph auxiliary information from CDS", "topics": [ "principal_graph_aux" ] }, { "page": "principal_graph_aux-cell_data_set-method", "title": "Method to extract principal graph auxiliary information from CDS", "topics": [ "principal_graph_aux,cell_data_set-method" ] }, { "page": "principal_graph_aux-set", "title": "Generic to set principal graph auxiliary information into CDS", "topics": [ "principal_graph_aux<-" ] }, { "page": "principal_graph_aux-set-cell_data_set-method", "title": "Method to set principal graph auxiliary information into CDS", "topics": [ "principal_graph_aux<-,cell_data_set-method" ] }, { "page": "principal_graph-cell_data_set-method", "title": "Method to extract principal graph from CDS", "topics": [ "principal_graph,cell_data_set-method" ] }, { "page": "principal_graph-set", "title": "Generic to set principal graph to CDS", "topics": [ "principal_graph<-" ] }, { "page": "principal_graph-set-cell_data_set-method", "title": "Generic to set principal graph to CDS", "topics": [ "principal_graph<-,cell_data_set-method" ] }, { "page": "pseudotime", "title": "Generic to extract pseudotime from CDS object", "topics": [ "pseudotime" ] }, { "page": "pseudotime-cell_data_set-method", "title": "Method to extract pseudotime from CDS object", "topics": [ "pseudotime,cell_data_set-method" ] }, { "page": "reduce_dimension", "title": "Compute a projection of a cell_data_set object into a lower dimensional space with non-linear dimension reduction methods", "topics": [ "reduce_dimension" ] }, { "page": "reduce_dimension_transform", "title": "Apply a reduce_dimension transform model to a cell_data_set.", "topics": [ "reduce_dimension_transform" ] }, { "page": "repmat", "title": "function to reproduce the behavior of repmat function in matlab to replicate and tile an matrix", "topics": [ "repmat" ] }, { "page": "save_monocle_objects", "title": "Save a Monocle3 full cell_data_set.", "topics": [ "save_monocle_objects" ] }, { "page": "save_transform_models", "title": "Save cell_data_set transform models.", "topics": [ "save_transform_models" ] }, { "page": "search_cds_nn_index", "title": "Search a nearest neighbor index that is stored in the cds.", "topics": [ "search_cds_nn_index" ] }, { "page": "search_nn_index", "title": "Search a nearest neighbor index.", "topics": [ "search_nn_index" ] }, { "page": "search_nn_matrix", "title": "Search a subject matrix for nearest neighbors to a query_matrix.", "topics": [ "search_nn_matrix" ] }, { "page": "set_cds_nn_index", "title": "Set a nearest neighor index in the cell_data_set.", "topics": [ "set_cds_nn_index" ] }, { "page": "set_cds_row_order_matrix", "title": "Set the row-major order counts matrix in the assays slot of the CDS when the CDS has a BPCells counts matrix.", "topics": [ "set_cds_row_order_matrix" ] }, { "page": "set_matrix_control", "title": "Verify and set the matrix_control parameter list.", "topics": [ "set_matrix_control" ] }, { "page": "set_nn_control", "title": "Verify and set nearest neighbor parameter list.", "topics": [ "set_nn_control" ] }, { "page": "size_factors", "title": "Get the size factors from a cds object.", "topics": [ "size_factors" ] }, { "page": "size_factors-set", "title": "Set the size factor values in the cell_data_set", "topics": [ "size_factors<-" ] }, { "page": "soft_assignment", "title": "Function to calculate the third term in the objective function", "topics": [ "soft_assignment" ] }, { "page": "sparse_prcomp_irlba", "title": "Principal Components Analysis", "topics": [ "sparse_prcomp_irlba" ] }, { "page": "top_markers", "title": "Identify the genes most specifically expressed in groups of cells", "topics": [ "top_markers" ] }, { "page": "transfer_cell_labels", "title": "Transfer cell column data from a reference to a query cell_data_set.", "topics": [ "transfer_cell_labels" ] } ], "_readme": "https://github.com/cole-trapnell-lab/monocle3/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assertthat", "assorthead", "base64enc", "batchelor", "beachmat", "beeswarm", "BH", "biglm", "Biobase", "BiocGenerics", "biocmake", "BiocNeighbors", "BiocParallel", "BiocSingular", "boot", "BPCells", "bslib", "cachem", "Cairo", "class", "classInt", "cli", "codetools", "commonmark", "cpp11", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "DelayedMatrixStats", "deldir", "digest", "dir.expiry", "distributional", "dplyr", "dqrng", "e1071", "evaluate", "farver", "fastmap", "filelock", "FNN", "fontawesome", "formatR", "fs", "furrr", "futile.logger", "futile.options", "future", "generics", "GenomicRanges", "ggbeeswarm", "ggdist", "ggforce", "ggplot2", "ggrastr", "ggrepel", "globals", "glue", "gridExtra", "gtable", "h5mread", "HDF5Array", "hexbin", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "igraph", "IRanges", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "leidenbase", "lifecycle", "limma", "listenv", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "minqa", "nlme", "nloptr", "numDeriv", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pbmcapply", "pheatmap", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "promises", "proxy", "pscl", "purrr", "quadprog", "R6", "ragg", "RANN", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppEigen", "RcppHNSW", "RcppProgress", "Rdpack", "reformulas", "reshape2", "ResidualMatrix", "rhdf5", "rhdf5filters", "Rhdf5lib", "RhpcBLASctl", "rlang", "rmarkdown", "rsample", "RSpectra", "rsvd", "Rtsne", "s2", "S4Arrays", "S4Vectors", "S7", "sass", "ScaledMatrix", "scales", "scattermore", "scuttle", "Seqinfo", "sf", "shiny", "SingleCellExperiment", "sitmo", "slam", "slider", "snow", "sourcetools", "sp", "SparseArray", "sparseMatrixStats", "spData", "spdep", "speedglm", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tinytex", "tweenr", "units", "utf8", "uwot", "vctrs", "vipor", "viridis", "viridisLite", "warp", "withr", "wk", "xfun", "xtable", "XVector", "yaml", "zoo" ], "_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": "monocle3-vignette.Rnw", "filename": "monocle3-vignette.pdf", "title": "Monocle3: Cell counting, differential expression, and trajectory analysis for single-cell RNA-Seq experiments", "engine": "knitr::knitr", "headings": [], "created": "2022-05-23 17:51:13", "modified": "2022-05-23 17:51:13", "commits": 1 } ], "_score": 9.79096351297987, "_indexed": false, "_nocasepkg": "monocle3", "_universes": [ "blaserlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.27", "date": "2026-06-03T06:52:29.000Z", "distro": "noble", "arch": "aarch64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "273cd28be52369ffc56d3e158700d69267e0297cd2b7defd667019d35adf662c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.7.0", "os": "linux", "version": "1.4.27", "date": "2026-06-03T06:52:37.000Z", "distro": "noble", "arch": "x86_64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "76c04c48f8d1714cf6662b11d071641846ed5f18c7ca7f3e465b1ba88ee2cb26", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.6.0", "os": "linux", "version": "1.4.27", "date": "2026-06-03T06:52:25.000Z", "distro": "noble", "arch": "aarch64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "645a2b5574a11cbba7fd178c9e1963f8f8212e411c7a7336afce12857965660c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.6.0", "os": "linux", "version": "1.4.27", "date": "2026-06-03T06:52:27.000Z", "distro": "noble", "arch": "x86_64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "428b30db72d0ae9e58981808098f79e18dda0bcd2c967e796115c74dde31343f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.5.3", "os": "mac", "version": "1.4.27", "date": "2026-06-03T06:51:02.000Z", "arch": "aarch64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "adf326078070725835ac8b9ba143d4463429af0c07bbbf053ad72f14873c28ed", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.5.3", "os": "mac", "version": "1.4.27", "date": "2026-06-03T06:52:13.000Z", "arch": "x86_64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "b53fbaf6721a867bd9644a9d80db37c045827842fe99a35579774eaad58edf9d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.6.0", "os": "mac", "version": "1.4.27", "date": "2026-06-03T06:55:07.000Z", "arch": "aarch64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "5721a61d9c54e6e460bb65f353e3032687d2a7771bdce271513dd6159b4b3c1a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.6.0", "os": "mac", "version": "1.4.27", "date": "2026-06-03T06:53:32.000Z", "arch": "x86_64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "07f0cfdbf95834b4fa3eac1e252794da6df9d33e13641ecf6c1e544af6e961c3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.27", "date": "2026-06-03T06:52:50.000Z", "arch": "emscripten", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "55e93f8d2a126f7b7e35792ce3d9d93729c4dca2838605634b6b19703a3a6748", "status": "success", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.7.0", "os": "win", "version": "1.4.27", "date": "2026-06-03T06:51:04.000Z", "arch": "x86_64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "dc7b86485f060c3b514d212947aa977c1c4010598d8da5b755bb2d7e6a9b9da6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.5.3", "os": "win", "version": "1.4.27", "date": "2026-06-03T06:51:09.000Z", "arch": "x86_64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "4a692dadd2d95721d3370adf75471966344a664692477a03dda54b4aefddecf5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" }, { "r": "4.6.0", "os": "win", "version": "1.4.27", "date": "2026-06-03T06:51:26.000Z", "arch": "x86_64", "commit": "536f1033d6de7c957f26a1f403f81efbd825e0db", "fileid": "dedc88e80a8a800386ceb5dd7bae8654bd3433d6851c9310842c8297fc48a246", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/blaserlab/actions/runs/26868334330" } ] }