Package: GeneNMF 0.6.0
GeneNMF: Non-Negative Matrix Factorization for Single-Cell Omics
A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Authors:
GeneNMF_0.6.0.tar.gz
GeneNMF_0.6.0.tar.gz(r-4.5-noble)GeneNMF_0.6.0.tar.gz(r-4.4-noble)
GeneNMF_0.6.0.tgz(r-4.4-emscripten)
GeneNMF.pdf |GeneNMF.html✨
GeneNMF/json (API)
NEWS
# Install 'GeneNMF' in R: |
install.packages('GeneNMF', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/carmonalab/genenmf/issues
- sampleObj - Sample dataset to test GeneNMF installation
Last updated 2 months agofrom:d7bb9ecb06. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 22 2024 |
R-4.5-linux | OK | Aug 22 2024 |
Exports:findVariableFeatures_wfiltersgetDataMatrixgetMetaProgramsgetNMFgenesmultiNMFmultiPCAplotMetaProgramsrunGSEArunNMF
Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestlsamagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmoSnowballCsourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisviridisLitewithrxfunxtableyamlzoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Find variable features | findVariableFeatures_wfilters |
Extract data matrix from Seurat object | getDataMatrix |
Extract consensus gene programs (meta-programs) | getMetaPrograms |
Get list of genes for each NMF program | getNMFgenes |
Run NMF on a list of Seurat objects | multiNMF |
Run PCA on a list of Seurat objects | multiPCA |
Visualizations for meta-programs | plotMetaPrograms |
Run Gene set enrichment analysis | runGSEA |
Compute NMF as a low-dim embedding for Seurat | runNMF |
Sample dataset to test GeneNMF installation | sampleObj |