scGraphVerse
scGraphVerse: A Gene Network Analysis Package
Bioconductor version: 3.23 · Package version: 1.2.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scGraphVerse")Details
| Maintainer | Francesco Cecere <francesco.cecerengs@gmail.com> |
| Author | Francesco Cecere [aut, cre] (ORCID: <https://orcid.org/0000-0002-0329-0870>), Annamaria Carissimo [aut], Daniela De Canditiis [aut], Claudia Angelini [aut, fnd] |
| License | GPL-3 + file LICENSE |
| URL | https://ngsFC.github.io/scGraphVerse |
| Bug Reports | https://github.com/ngsFC/scGraphVerse/issues |
| System Requirements | Python (>= 3.6) and arboreto Python package for GRNBoost2 method. Use init_py(install_missing = TRUE) for automated installation. |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneRegulation, GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, NetworkInference, Pathways, RNASeq, Reactome, Sequencing, SingleCell, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/scGraphVerse/ |
Citation
From within R, enter 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 1.2.0, https://bioconductor.org/packages/scGraphVerse.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- scGraphVerse Case Study: B-cell GRN Reconstruction
- scGraphVerse Case Study: Zero-Inflated Simulation and GRN Inference
Download
Follow the installation instructions to use this package in your R session.
| Source package | scGraphVerse_1.2.0.tar.gz |
| macOS binary (arm64) | scGraphVerse_1.2.0.tgz |
| macOS binary (x86_64) | scGraphVerse_1.2.0.tgz |
Dependencies
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
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