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soGGi

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("soGGi")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
soggi PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Coverage, Sequencing, Software
Version 1.34.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL (>= 3)
Depends R (>= 3.5.0), BiocGenerics, SummarizedExperiment
Imports methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel
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Package Archives

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

Source Package soGGi_1.34.0.tar.gz
Windows Binary soGGi_1.34.0.zip (64-bit only)
macOS Binary (x86_64) soGGi_1.34.0.tgz
macOS Binary (arm64) soGGi_1.34.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/soGGi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/soGGi
Bioc Package Browser https://code.bioconductor.org/browse/soGGi/
Package Short Url https://bioconductor.org/packages/soGGi/
Package Downloads Report Download Stats