scGraphVerse

This is the released version of scGraphVerse; for the devel version, see scGraphVerse.

scGraphVerse: A Gene Network Analysis Package

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DOI: 10.18129/B9.bioc.scGraphVerse

Bioconductor version: Release (3.22)

A package for inferring, comparing, and visualizing gene networks from single-cell RNA sequencing data. It integrates multiple methods (GENIE3, GRNBoost2, ZILGM, PCzinb, and JRF) for robust network inference, supports consensus building across methods or datasets, and provides tools for evaluating regulatory structure and community similarity. GRNBoost2 requires Python package 'arboreto' which can be installed using init_py(install_missing = TRUE). This package includes adapted functions from ZILGM (Park et al., 2021), JRF (Petralia et al., 2015), and learn2count (Nguyen et al. 2023) packages with proper attribution under GPL-2 license.

Author: Francesco Cecere [aut, cre] ORCID iD ORCID: 0000-0002-0329-0870 , Annamaria Carissimo [aut], Daniela De Canditiis [aut], Claudia Angelini [aut, fnd]

Maintainer: Francesco Cecere <francesco.cecerengs at gmail.com>

Citation (from within R, enter citation("scGraphVerse")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("scGraphVerse")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scGraphVerse")

scGraphVerse Case Study: B-cell GRN Reconstruction HTML R Script

scGraphVerse Simulation Study: Sim & GRN Reconstruction HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneRegulation, GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, NetworkInference, Pathways, RNASeq, Reactome, Sequencing, SingleCell, Software, Visualization

Version 1.0.0

In Bioconductor since BioC 3.22 (R-4.5) (< 6 months)

License GPL-3 + file LICENSE

Depends R (>= 4.5.0)

Imports BiocBaseUtils, BiocParallel(>= 1.30.0), doParallel, doRNG, GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, distributions3, dplyr, grDevices, graphics, httr, igraph, jsonlite, methods, parallel, reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors, graph, mpath

System Requirements Python (>= 3.6) and arboreto Python package for GRNBoost2 method. Use init_py(install_missing = TRUE) for automated installation.

URL https://ngsFC.github.io/scGraphVerse

Bug Reports https://github.com/ngsFC/scGraphVerse/issues

Suggests AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot, fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db, org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA, rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0), knitr, rmarkdown, tidyverse, magick, celldex, SingleR, TENxPBMCData, scater, GenomeInfoDb, GenomicRanges

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scGraphVerse_1.0.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) scGraphVerse_1.0.0.tgz

macOS Binary (arm64) scGraphVerse_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/scGraphVerse

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scGraphVerse

Bioc Package Browser https://code.bioconductor.org/browse/scGraphVerse/

Package Short Url https://bioconductor.org/packages/scGraphVerse/

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