Package: fastglmpca 0.1-103

Eric Weine

fastglmpca: Fast Algorithms for Generalized Principal Component Analysis

Implements fast, scalable optimization algorithms for fitting generalized principal components analysis (GLM-PCA) models, as described in "A Generalization of Principal Components Analysis to the Exponential Family" Collins M, Dasgupta S, Schapire RE (2002, ISBN:9780262271738), and subsequently "Feature Selection and Dimension Reduction for Single-Cell RNA-Seq Based on a Multinomial Model" Townes FW, Hicks SC, Aryee MJ, Irizarry RA (2019) <doi:10.1186/s13059-019-1861-6>.

Authors:Eric Weine [aut, cre], Peter Carbonetto [aut], Matthew Stephens [aut]

fastglmpca_0.1-103.tar.gz
fastglmpca_0.1-103.tar.gz(r-4.5-noble)fastglmpca_0.1-103.tar.gz(r-4.4-noble)
fastglmpca_0.1-103.tgz(r-4.4-emscripten)fastglmpca_0.1-103.tgz(r-4.3-emscripten)
fastglmpca.pdf |fastglmpca.html✨
fastglmpca/json (API)
NEWS

# Install 'fastglmpca' in R:

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

Bug tracker:https://github.com/stephenslab/fastglmpca/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

pbmc_facs - Mixture of 10 FACS-purified PBMC Single-Cell RNA-seq data

2.00 score 9 scripts 200 downloads 5 exports 13 dependencies

Last updated 9 months agofrom:44a29924cc. Checks:OK: 1 NOTE: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 01 2024
R-4.5-linux-x86_64	NOTE	Oct 01 2024

Exports:fit_glmpca_pois fit_glmpca_pois_control_default generate_glmpca_data_pois init_glmpca_pois set_fastglmpca_threads

Dependencies:daarem distr float lattice MASS Matrix MatrixExtra Rcpp RcppArmadillo RcppParallel RhpcBLASctl sfsmisc startupmsg

Analysis of single-cell RNA-seq data using fastglmpca

Eric Weine and Peter Carbonetto

Rendered fromintro_fastglmpca.Rmdusingknitr::rmarkdownon Oct 01 2024.

Last update: 2024-02-01
Started: 2024-02-01

Citation

Readme and manuals

Help Manual

Help page	Topics
Fit Poisson GLM-PCA Model to Count Data	fit_glmpca_pois fit_glmpca_pois_control_default init_glmpca_pois
Get Fitted Values for GLM-PCA Model Fit	fitted.glmpca_pois_fit
Generate Data from a GLMCPA Model	generate_glmpca_data_pois
Mixture of 10 FACS-purified PBMC Single-Cell RNA-seq data	pbmc_facs
Set up Multithreading for fastglmpca	set_fastglmpca_threads
Summarize GLM-PCA Model Fit	print.summary.glmpca_pois_fit summary.glmpca_pois_fit