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tidyCoverage

This is the development version of tidyCoverage; for the stable release version, see tidyCoverage.

Extract and aggregate genomic coverage over features of interest


Bioconductor version: Development (3.20)

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

Citation (from within R, enter citation("tidyCoverage")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("tidyCoverage")

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("tidyCoverage")
Introduction to tidyCoverage HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Coverage, Sequencing, Software
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3.0), SummarizedExperiment
Imports S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, dplyr, fansi, pillar, rlang, cli, purrr, vctrs, stats
System Requirements
URL https://github.com/js2264/tidyCoverage
Bug Reports https://github.com/js2264/tidyCoverage/issues
See More
Suggests tidySummarizedExperiment, plyranges, ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package tidyCoverage_1.1.0.tar.gz
Windows Binary tidyCoverage_1.1.0.zip (64-bit only)
macOS Binary (x86_64) tidyCoverage_1.1.0.tgz
macOS Binary (arm64) tidyCoverage_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tidyCoverage
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tidyCoverage
Bioc Package Browser https://code.bioconductor.org/browse/tidyCoverage/
Package Short Url https://bioconductor.org/packages/tidyCoverage/
Package Downloads Report Download Stats