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 (3.24)
`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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| LICENSE | Text |
Details
| biocViews | Coverage, Sequencing, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://github.com/js2264/tidyCoverage |
| Bug Reports | https://github.com/js2264/tidyCoverage/issues |
See More
| Suggests | tidySummarizedExperiment, plyranges, TxDb.Mmusculus.UCSC.mm10.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_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | tidyCoverage_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | tidyCoverage_1.9.0.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 |