tidyCoverage

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

Extract and aggregate genomic coverage over features of interest

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DOI: 10.18129/B9.bioc.tidyCoverage

Bioconductor version: Release (3.22)

`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 "4.5") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, Sequencing, Software

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License MIT + file LICENSE

Depends R (>= 4.3.0), SummarizedExperiment

Imports S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, ggplot2, dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats

System Requirements

URL https://github.com/js2264/tidyCoverage

Bug Reports https://github.com/js2264/tidyCoverage/issues

Suggests tidySummarizedExperiment, plyranges, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0)

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Package Archives

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

Source Package tidyCoverage_1.6.0.tar.gz

Windows Binary (x86_64) tidyCoverage_1.5.0.zip

macOS Binary (x86_64) tidyCoverage_1.6.0.tgz

macOS Binary (arm64) tidyCoverage_1.6.0.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/

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