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

 

Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

Bioconductor version: Release (3.5)

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")

 

PDF R Script soggi
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Coverage, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License GPL (>= 3)
Depends R (>= 3.2.0), BiocGenerics, SummarizedExperiment
Imports methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel
LinkingTo
Suggests testthat, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me DChIPRep
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source soGGi_1.8.0.tar.gz
Windows Binary soGGi_1.8.0.zip
Mac OS X 10.11 (El Capitan) soGGi_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/soGGi/tree/release-3.5
Package Short Url http://bioconductor.org/packages/soGGi/
Package Downloads Report Download Stats

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