To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("soGGi")
In most cases, you don't need to download the package archive at all.
soGGi
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see soGGi.
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
Bioconductor version: 3.2
The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.
Author: Gopuraja Dharmalingam, Tom Carroll
Maintainer: Tom Carroll <tc.infomatics at gmail.com>
Citation (from within R,
enter citation("soGGi")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("soGGi")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("soGGi")
| soggi | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, Coverage, Sequencing, Software |
| Version | 1.2.1 |
| In Bioconductor since | BioC 3.1 (R-3.2) (1 year) |
| License | GPL (>= 3) |
| Depends | R (>= 3.2.0), BiocGenerics |
| Imports | methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment(>= 0.2.0), Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel |
| LinkingTo | |
| Suggests | testthat, BiocStyle, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | soGGi_1.2.1.tar.gz |
| Windows Binary | soGGi_1.2.1.zip |
| Mac OS X 10.6 (Snow Leopard) | soGGi_1.2.1.tgz |
| Mac OS X 10.9 (Mavericks) | soGGi_1.2.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/soGGi/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/soGGi/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
