genomation
Summary, annotation and visualization of genomic data
Bioconductor version: Release (3.17)
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.
Author: Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons [ctb], Bozena Mika-Gospodorz [ctb]
Maintainer: Altuna Akalin <aakalin at gmail.com>, Vedran Franke <vedran.franke at gmail.com>, Katarzyna Wreczycka <katwre at gmail.com>
citation("genomation")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("genomation")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("genomation")| genomation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, CpGIsland, Sequencing, Software, Visualization |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), grid |
| Imports | Biostrings(>= 2.47.6), BSgenome(>= 1.47.3), data.table, GenomeInfoDb, 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) |
| Linking To | Rcpp |
| Suggests | BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit |
| System Requirements | |
| Enhances | |
| URL | http://bioinformatics.mdc-berlin.de/genomation/ |
| Bug Reports | https://github.com/BIMSBbioinfo/genomation/issues |
See More
| Depends On Me | |
| Imports Me | CexoR, EpiCompare, fCCAC, RCAS |
| Suggests Me | methylKit |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | genomation_1.32.0.tar.gz |
| Windows Binary | genomation_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | genomation_1.32.0.tgz |
| macOS Binary (arm64) | genomation_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/genomation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/genomation |
| Bioc Package Browser | https://code.bioconductor.org/browse/genomation/ |
| Package Short Url | https://bioconductor.org/packages/genomation/ |
| Package Downloads Report | Download Stats |