genomation
Summary, annotation and visualization of genomic data
Bioconductor version: 3.23 · Package version: 1.44.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("genomation")Details
| Maintainer | Altuna Akalin <aakalin@gmail.com>, Vedran Franke <vedran.franke@gmail.com>, Katarzyna Wreczycka <katwre@gmail.com> |
| Author | Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons [ctb], Bozena Mika-Gospodorz [ctb] |
| License | Artistic-2.0 |
| URL | http://bioinformatics.mdc-berlin.de/genomation/ |
| Bug Reports | https://github.com/BIMSBbioinfo/genomation/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, CpGIsland, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/genomation/ |
Citation
From within R, enter citation("genomation"):
Altuna Akalin, Vedran Franke, Katarzyna Wreczycka. genomation: Summary, annotation and visualization of genomic data. doi:10.18129/B9.bioc.genomation, R package version 1.44.0, https://bioconductor.org/packages/genomation.
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 | genomation_1.44.0.tar.gz |
| Windows binary (x86_64) | genomation_1.44.0.zip |
| macOS binary (arm64) | genomation_1.44.0.tgz |
| macOS binary (x86_64) | genomation_1.44.0.tgz |
Dependencies
Depends: R (>= 3.5.0), grid
Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, Seqinfo, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14)
LinkingTo: Rcpp
Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit
Reverse dependencies
Imports Me (5): CexoR, EpiCompare, fCCAC, GenomicPlot, RCAS
Suggests Me (1): methylKit