scGraphVerse
This is the development version of scGraphVerse; for the stable release version, see scGraphVerse.
scGraphVerse: A Gene Network Analysis Package
Bioconductor version: Development (3.24)
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] 
, Annamaria Carissimo [aut], Daniela De Canditiis [aut], Claudia Angelini [aut, fnd]
Maintainer: Francesco Cecere <francesco.cecerengs at gmail.com>
citation("scGraphVerse")):Francesco Cecere, Annamaria Carissimo, Daniela De Canditiis, Claudia Angelini. scGraphVerse: scGraphVerse: A Gene Network Analysis Package. doi:10.18129/B9.bioc.scGraphVerse, R package version 1.3.0, https://bioconductor.org/packages/scGraphVerse.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneRegulation, GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, NetworkInference, Pathways, RNASeq, Reactome, Sequencing, SingleCell, Software, Visualization |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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 |
See More
| 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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| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scGraphVerse_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | scGraphVerse_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | scGraphVerse_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scGraphVerse |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scGraphVerse |
| Package Short Url | https://bioconductor.org/packages/scGraphVerse/ |
| Package Downloads Report | Download Stats |