epistack
This is the development version of epistack; for the stable release version, see epistack.
Heatmaps of Stack Profiles from Epigenetic Signals
Bioconductor version: Development (3.24)
The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.
Author: SACI Safia [aut], DEVAILLY Guillaume [cre, aut]
Maintainer: DEVAILLY Guillaume <gdevailly at hotmail.com>
citation("epistack")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("epistack")
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("epistack")| Using epistack | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChIPSeq, Coverage, GeneExpression, Preprocessing, RNASeq, Software |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods |
| System Requirements | |
| URL | https://github.com/GenEpi-GenPhySE/epistack |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick |
| 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 | epistack_1.19.0.tar.gz |
| Windows Binary (x86_64) | epistack_1.19.0.zip |
| macOS Binary (big-sur-x86_64) | epistack_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | epistack_1.19.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epistack |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epistack |
| Bioc Package Browser | https://code.bioconductor.org/browse/epistack/ |
| Package Short Url | https://bioconductor.org/packages/epistack/ |
| Package Downloads Report | Download Stats |