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https://github.com/fertiglab/cogaps

Bayesian MCMC matrix factorization algorithm

https://github.com/fertiglab/cogaps

Science Score: 26.0%

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    Low similarity (12.5%) to scientific vocabulary

Keywords

bayesian-inference bioinformatics human-cell-atlas machine-learning non-negative-matrix-factorization single-cell-rna-seq
Last synced: 6 months ago · JSON representation

Repository

Bayesian MCMC matrix factorization algorithm

Basic Info
Statistics
  • Stars: 69
  • Watchers: 12
  • Forks: 16
  • Open Issues: 24
  • Releases: 0
Topics
bayesian-inference bioinformatics human-cell-atlas machine-learning non-negative-matrix-factorization single-cell-rna-seq
Created over 10 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

R build status

CoGAPS

Bioc downloads

Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

Installing CoGAPS

Via Bioconductor:

install.packages("BiocManager") BiocManager::install("FertigLab/CoGAPS")

The most up-to-date version of CoGAPS can be installed directly from the FertigLab Github Repository:

devtools::install_github("FertigLab/CoGAPS")

Using CoGAPS

Follow the vignette here and available as static html here

Run as nextflow pipeline

The example below will attempt running CoGAPS with number of patterns 3 and 4 on every .rds and .h5ad file in the input folder (tests/nextflow). nextflow run main.nf --input tests/nextflow --outdir out -c nextflow.config -profile docker --max_memory 10GB --npatterns 3,4

Supported CLI params and their defaults are:

npatterns = "5"
nsets = 1
niterations = 100
sparse = 0
seed = 42
distributed = "null"
nthreads = 1
max_memory = '128.GB'
max_cpus = 8
max_time = '72.h'
n_top_genes = 5000

Owner

  • Name: FertigLab
  • Login: FertigLab
  • Kind: organization
  • Email: ejfertig@jhmi.edu

Software projects in computational biology and bioinformatics in Elana Fertig's lab in Oncology Biostatistics and Bioinformatics at JHMI

GitHub Events

Total
  • Issues event: 19
  • Watch event: 4
  • Delete event: 12
  • Issue comment event: 30
  • Push event: 213
  • Pull request review comment event: 9
  • Pull request review event: 13
  • Pull request event: 26
  • Create event: 13
Last Year
  • Issues event: 19
  • Watch event: 4
  • Delete event: 12
  • Issue comment event: 30
  • Push event: 213
  • Pull request review comment event: 9
  • Pull request review event: 13
  • Pull request event: 26
  • Create event: 13

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 36
  • Total pull requests: 30
  • Average time to close issues: 5 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 12
  • Total pull request authors: 5
  • Average comments per issue: 1.56
  • Average comments per pull request: 0.83
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 16
  • Average time to close issues: 14 days
  • Average time to close pull requests: 2 days
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.81
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • dimalvovs (20)
  • LiuCanidk (4)
  • mumdark (3)
  • mperezrodriguez (1)
  • dtatarak (1)
  • parkerstevenson (1)
  • dm8000 (1)
  • favorov (1)
  • kwoyshner (1)
  • jmitchell81 (1)
  • grimbough (1)
  • rpalaganas (1)
Pull Request Authors
  • dimalvovs (24)
  • jmitchell81 (3)
  • ejfertig (1)
  • jeanettejohnson (1)
  • JamesFrifan (1)
Top Labels
Issue Labels
question (6) bug (1)
Pull Request Labels
bug (1)

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • BiocParallel * imports
  • RColorBrewer * imports
  • Rcpp * imports
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • cluster * imports
  • gplots * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • rhdf5 * imports
  • stats * imports
  • tools * imports
  • utils * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests