tidyCoverage
Extract and aggregate genomic coverage over features of interest
Bioconductor version: 3.23 · Package version: 1.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
`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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidyCoverage")Details
| Maintainer | Jacques Serizay <jacquesserizay@gmail.com> |
| Author | Jacques Serizay [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/js2264/tidyCoverage |
| Bug Reports | https://github.com/js2264/tidyCoverage/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/tidyCoverage/ |
Citation
From within R, enter citation("tidyCoverage"):
Jacques Serizay. tidyCoverage: Extract and aggregate genomic coverage over features of interest. doi:10.18129/B9.bioc.tidyCoverage, R package version 1.8.0, https://bioconductor.org/packages/tidyCoverage.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | tidyCoverage_1.8.0.tar.gz |
| Windows binary (x86_64) | tidyCoverage_1.7.0.zip |
| macOS binary (arm64) | tidyCoverage_1.8.0.tgz |
| macOS binary (x86_64) | tidyCoverage_1.8.0.tgz |
Dependencies
Depends: R (>= 4.3.0), SummarizedExperiment
Imports: S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, tibble, ggplot2, ggrastr, dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats
Suggests: tidySummarizedExperiment, plyranges, TxDb.Mmusculus.UCSC.mm10.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0)