Package: GeneNMF 0.9.5

Massimo Andreatta

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:Massimo Andreatta [aut, cre], Santiago Carmona [aut]

GeneNMF_0.9.5.tar.gz
GeneNMF_0.9.5.zip(r-4.7)GeneNMF_0.9.5.zip(r-4.6)GeneNMF_0.9.5.zip(r-4.5)
GeneNMF_0.9.5.tgz(r-4.6-any)GeneNMF_0.9.5.tgz(r-4.5-any)
GeneNMF_0.9.5.tar.gz(r-4.7-any)GeneNMF_0.9.5.tar.gz(r-4.6-any)
GeneNMF_0.9.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeneNMF/json (API)

# Install 'GeneNMF' in R:

install.packages('GeneNMF', repos = c('https://carmonalab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/carmonalab/genenmf/issues

Datasets:

sampleObj - Sample dataset to test GeneNMF installation

On CRAN:

7.89 score 189 stars 51 scripts 715 downloads 9 exports 149 dependencies

Last updated from:355c466473. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	284
source / vignettes	OK	269
linux-release-x86_64	OK	259
macos-release-arm64	OK	180
macos-oldrel-arm64	OK	195
windows-devel	OK	245
windows-release	OK	211
windows-oldrel	OK	262
wasm-release	OK	170

Exports:dropMetaPrograms findVariableFeatures_wfilters getDataMatrix getMetaPrograms getNMFgenes multiNMF plotMetaPrograms runGSEA runNMF

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crosstalk curl data.table deldir dendextend digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest lsa magrittr MASS Matrix matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pheatmap pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S7 sass scales scattermore sctransform Seurat SeuratObject shiny sitmo SnowballC sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridis viridisLite withr xfun xtable yaml zoo

Index of GeneNMF vignettes

Rendered frommake.index.Rmdusingknitr::rmarkdown

Last update: 2024-07-19
Started: 2024-02-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Drop meta-programs	dropMetaPrograms
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
Visualizations for meta-programs	plotMetaPrograms
Run gene-set overrepresentation analysis	runGSEA
Compute NMF as a low-dim embedding for Seurat	runNMF
Sample dataset to test GeneNMF installation	sampleObj