soGGi

DOI: 10.18129/B9.bioc.soGGi    

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

Bioconductor version: Release (3.11)

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, Doug Barrows, Tom Carroll

Maintainer: Tom Carroll <tc.infomatics at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("soGGi")

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("soGGi")

 

PDF	R Script	soggi
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Coverage, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 3.1 (R-3.2) (5.5 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, profileplyr
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	soGGi_1.20.0.tar.gz
Windows Binary	soGGi_1.20.0.zip
macOS 10.13 (High Sierra)	soGGi_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/soGGi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/soGGi
Package Short Url	https://bioconductor.org/packages/soGGi/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive