scGraphVerse
This is the development version of scGraphVerse; to use it, please install the devel version of Bioconductor.
scGraphVerse: A Gene Regulatory Network Analysis Package
Bioconductor version: Development (3.22)
A package for inferring, comparing, and visualizing gene regulatory 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")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scGraphVerse")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GeneRegulation, GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, NetworkInference, Pathways, RNASeq, Reactome, Sequencing, SingleCell, Software, Visualization |
| Version | 0.99.19 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| 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, 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 |
| Linking To | |
| Enhances | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | scGraphVerse_0.99.19.tgz |
| macOS Binary (arm64) | scGraphVerse_0.99.19.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/ |
| Package Downloads Report | Download Stats |