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Bioconductor - recoup

recoup

This is the released version of recoup; for the devel version, see recoup.

An R package for the creation of complex genomic profile plots

Bioconductor version: Release (3.21)

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

Author: Panagiotis Moulos <moulos at fleming.gr>

Maintainer: Panagiotis Moulos <moulos at fleming.gr>

Citation (from within R, enter citation("recoup")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("recoup")

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("recoup")
Details biocViews ATACSeq, Alignment, ChIPSeq, ChipOnChip, Coverage, DataImport, GeneExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software Version 1.36.0 In Bioconductor since BioC 3.3 (R-3.3) (9 years) License GPL (>= 3) Depends R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap Imports BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, txdbmaker, utils System Requirements URL https://github.com/pmoulos/recoup See More Package Archives

Follow Installation instructions to use this package in your R session.

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