tidyCoverage
Extract and aggregate genomic coverage over features of interest
Bioconductor version: Release (3.19)
`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("tidyCoverage")):
Installation
To install this package, start R (version "4.4") 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 | ||
| LICENSE | Text |
Details
| biocViews | Coverage, Sequencing, Software |
| Version | 1.0.0 |
| 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidyCoverage_1.0.0.tar.gz |
| Windows Binary (x86_64) | tidyCoverage_1.0.0.zip |
| macOS Binary (x86_64) | tidyCoverage_1.0.0.tgz |
| macOS Binary (arm64) | tidyCoverage_1.0.0.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 |
| Old Source Packages for BioC 3.19 | Source Archive |