Package: monocle3 1.3.7
monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq
Monocle 3 performs clustering, differential expression and trajectory analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle 3 also performs differential expression analysis, clustering, visualization, and other useful tasks on single-cell expression data. It is designed to work with RNA-Seq data, but could be used with other types as well.
Authors:
monocle3_1.3.7.tar.gz
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monocle3.pdf |monocle3.html✨
monocle3/json (API)
NEWS
# Install 'monocle3' in R: |
install.packages('monocle3', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cole-trapnell-lab/monocle3/issues
Last updated 5 months agofrom:98402ed0c1. Checks:OK: 1 ERROR: 8. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 30 2024 |
R-4.5-win-x86_64 | ERROR | Aug 30 2024 |
R-4.5-linux-x86_64 | ERROR | Aug 30 2024 |
R-4.4-win-x86_64 | ERROR | Aug 30 2024 |
R-4.4-mac-x86_64 | ERROR | Aug 30 2024 |
R-4.4-mac-aarch64 | ERROR | Aug 30 2024 |
R-4.3-win-x86_64 | ERROR | Aug 30 2024 |
R-4.3-mac-x86_64 | ERROR | Aug 30 2024 |
R-4.3-mac-aarch64 | ERROR | Aug 30 2024 |
Exports:aggregate_gene_expressionalign_cdsalign_transformchoose_cellschoose_graph_segmentsclear_cds_slotscluster_cellsclusterscoefficient_tablecombine_cdscompare_modelsdetect_genesestimate_size_factorsevaluate_fitsexprsfDatafData<-find_gene_modulesfit_modelsfix_missing_cell_labelsgenerate_garnett_marker_fileget_citationsgraph_testidentity_tablelearn_graphload_a549load_cellranger_dataload_mm_dataload_monocle_objectsload_mtx_dataload_transform_modelsload_worm_embryoload_worm_l2make_cds_nn_indexmake_nn_indexmodel_predictionsnew_cell_data_setnormalized_countsorder_cellspartitionspDatapData<-plot_cellsplot_cells_3dplot_genes_by_groupplot_genes_in_pseudotimeplot_genes_violinplot_pc_variance_explainedplot_percent_cells_positivepreprocess_cdspreprocess_transformprincipal_graphprincipal_graph_auxprincipal_graph_aux<-principal_graph<-pseudotimereduce_dimensionreduce_dimension_transformsave_monocle_objectssave_transform_modelssearch_cds_nn_indexsearch_nn_indexsearch_nn_matrixset_cds_nn_indexsize_factorstop_markerstransfer_cell_labels
Dependencies:abindaskpassassertthatbase64encbatchelorbeachmatbeeswarmBHbiglmBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbootbslibcachemCairoclassclassIntclicodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDelayedMatrixStatsdeldirdigestdplyrdqrnge1071evaluatefansifarverfastmapFNNfontawesomeformatRfsfurrrfutile.loggerfutile.optionsfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelglobalsgluegridExtragrrgtableHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenbaselifecyclelimmalistenvlme4lmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamunsellnlmenloptropensslparallellypbapplypbmcapplypheatmappillarpkgconfigplotlyplyrpngpromisesproxypsclpurrrR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppHNSWRcppProgressreshape2ResidualMatrixrhdf5rhdf5filtersRhdf5libRhpcBLASctlrlangrmarkdownrsampleRSpectrarsvdRtsnes2S4ArraysS4VectorssassScaledMatrixscalesscuttlesfshinySingleCellExperimentsitmoslamslidersnowsourcetoolsspSparseArraysparseMatrixStatsspDataspdepspeedglmstatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttinytexUCSC.utilsunitsutf8uwotvctrsviporviridisviridisLitewarpwithrwkxfunxtableXVectoryamlzlibbioczoo