Package: GeneNMF 0.6.2

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_0.6.2.tar.gz
GeneNMF_0.6.2.zip(r-4.5)GeneNMF_0.6.2.zip(r-4.4)GeneNMF_0.6.2.zip(r-4.3)
GeneNMF_0.6.2.tgz(r-4.5-any)GeneNMF_0.6.2.tgz(r-4.4-any)GeneNMF_0.6.2.tgz(r-4.3-any)
GeneNMF_0.6.2.tar.gz(r-4.5-noble)GeneNMF_0.6.2.tar.gz(r-4.4-noble)
GeneNMF_0.6.2.tgz(r-4.4-emscripten)
GeneNMF.pdf |GeneNMF.html✨
GeneNMF/json (API)
NEWS

# 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:

6.72 score 98 stars 12 scripts 598 downloads 10 exports 152 dependencies

Last updated 3 months agofrom:d74e025400. Checks:6 OK, 2 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 09 2025
R-4.5-win	OK	Feb 09 2025
R-4.5-mac	OK	Feb 09 2025
R-4.5-linux	OK	Feb 09 2025
R-4.4-win	OK	Feb 09 2025
R-4.4-mac	OK	Feb 09 2025
R-4.3-win	NOTE	Feb 09 2025
R-4.3-mac	NOTE	Feb 09 2025

Exports:dropMetaPrograms findVariableFeatures_wfilters getDataMatrix getMetaPrograms getNMFgenes multiNMF multiPCA plotMetaPrograms runGSEA runNMF

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table deldir dendextend digest dotCall64 dplyr dqrng evaluate fansi 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 leidenbase lifecycle listenv lmtest lsa magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell nlme openssl 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 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

M. Andreatta, S. Carmona

Rendered frommake.index.Rmdusingknitr::rmarkdownon Feb 09 2025.

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
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