Package: fastglmpca 0.1-106

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]

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fastglmpca.pdf |fastglmpca.html✨
fastglmpca/json (API)
NEWS

# Install 'fastglmpca' in R:
install.packages('fastglmpca', repos = c('https://stephenslab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On CRAN:

5 exports 9 stars 2.50 score 13 dependencies 9 scripts 195 downloads

Last updated 26 days agofrom:ba8427e3f7. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 23 2024
R-4.5-win-x86_64NOTEAug 23 2024
R-4.5-linux-x86_64NOTEAug 23 2024
R-4.4-win-x86_64NOTEAug 23 2024
R-4.4-mac-x86_64NOTEAug 23 2024
R-4.4-mac-aarch64NOTEAug 23 2024
R-4.3-win-x86_64NOTEAug 23 2024
R-4.3-mac-x86_64NOTEAug 23 2024
R-4.3-mac-aarch64NOTEAug 23 2024

Exports:fit_glmpca_poisfit_glmpca_pois_control_defaultgenerate_glmpca_data_poisinit_glmpca_poisset_fastglmpca_threads

Dependencies:daaremdistrfloatlatticeMASSMatrixMatrixExtraRcppRcppArmadilloRcppParallelRhpcBLASctlsfsmiscstartupmsg

Analysis of single-cell RNA-seq data using fastglmpca

Eric Weine and Peter Carbonetto

Rendered fromintro_fastglmpca.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2024-01-23
Started: 2023-11-09

Readme and manuals

Help Manual

Help pageTopics
Fit Poisson GLM-PCA Model to Count Datafit_glmpca_pois fit_glmpca_pois_control_default init_glmpca_pois
Get Fitted Values for GLM-PCA Model Fitfitted.glmpca_pois_fit
Generate Data from a GLM-PCA Modelgenerate_glmpca_data_pois
Mixture of 10 FACS-purified PBMC Single-Cell RNA-seq datapbmc_facs
Set up Multithreading for fastglmpcaset_fastglmpca_threads
Summarize GLM-PCA Model Fitprint.summary.glmpca_pois_fit summary.glmpca_pois_fit