recoup
An R package for the creation of complex genomic profile plots
Bioconductor version: Release (3.20)
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("recoup")):
Installation
To install this package, start R (version "4.4") 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")| Introduction to the recoup package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Alignment, ChIPSeq, ChipOnChip, Coverage, DataImport, GeneExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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
| Suggests | grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL |
| 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 | recoup_1.34.0.tar.gz |
| Windows Binary (x86_64) | recoup_1.34.0.zip |
| macOS Binary (x86_64) | recoup_1.34.0.tgz |
| macOS Binary (arm64) | recoup_1.33.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/recoup |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/recoup |
| Bioc Package Browser | https://code.bioconductor.org/browse/recoup/ |
| Package Short Url | https://bioconductor.org/packages/recoup/ |
| Package Downloads Report | Download Stats |