DOI: 10.18129/B9.bioc.genomation
Summary, annotation and visualization of genomic data
Bioconductor version: Release (3.6)
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 (from within R,
enter citation("genomation")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("genomation")
Documentation
Details
| biocViews | Annotation, CpGIsland, Sequencing, Software, Visualization |
| Version | 1.11.3 |
| In Bioconductor since | BioC 3.1 (R-3.2) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0), grid |
| Imports | Biostrings, BSgenome, data.table, GenomeInfoDb, GenomicRanges(>= 1.23.26), GenomicAlignments, S4Vectors(>= 0.9.25), ggplot2, gridBase, impute, IRanges, matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools(>= 1.25.2), seqPattern, rtracklayer, RUnit, Rcpp (>= 0.12.14) |
| LinkingTo | Rcpp |
| Suggests | BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown |
| SystemRequirements | |
| Enhances | |
| URL | bioinformatics.mdc-berlin.de/genomation/ |
| BugReports | github.com/BIMSBbioinfo/genomation/issues |
| Depends On Me | |
| Imports Me | CexoR, fCCAC, RCAS |
| Suggests Me | methylKit |
| Build Report |
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