epiregulon.extra
This is the released version of epiregulon.extra; for the devel version, see epiregulon.extra.
Companion package to epiregulon with additional plotting, differential and graph functions
Bioconductor version: Release (3.23)
Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.
Author: Xiaosai Yao [aut, cre]
, Tomasz Włodarczyk [aut]
, Timothy Keyes [aut], Shang-Yang Chen [aut]
Maintainer: Xiaosai Yao <xiaosai.yao at gmail.com>
citation("epiregulon.extra")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("epiregulon.extra")
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("epiregulon.extra")| Data visualization with epiregulon.extra | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChipOnChip, DifferentialExpression, GeneExpression, GeneRegulation, GeneTarget, GraphAndNetwork, Network, Normalization, Software, Transcription |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4), SingleCellExperiment |
| Imports | scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, patchwork, reshape2, scales, scater |
| System Requirements | |
| URL | https://github.com/xiaosaiyao/epiregulon.extra/ |
| Bug Reports | https://github.com/xiaosaiyao/epiregulon.extra/issues |
See More
| Suggests | epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), msigdb, GSEABase, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | epiregulon.extra_1.8.0.tar.gz |
| Windows Binary (x86_64) | epiregulon.extra_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | epiregulon.extra_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | epiregulon.extra_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epiregulon.extra |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epiregulon.extra |
| Bioc Package Browser | https://code.bioconductor.org/browse/epiregulon.extra/ |
| Package Short Url | https://bioconductor.org/packages/epiregulon.extra/ |
| Package Downloads Report | Download Stats |