soGGi
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last 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: Release (3.23)
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("soGGi")):Gopuraja Dharmalingam, Doug Barrows, Tom Carroll. soGGi: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals. doi:10.18129/B9.bioc.soGGi, R package version 1.44.0, https://bioconductor.org/packages/soGGi.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | |
| Reference Manual |
Details
| biocViews | ChIPSeq, Coverage, Sequencing, Software |
| Version | 1.44.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.5.0), BiocGenerics, SummarizedExperiment |
| Imports | methods, reshape2, ggplot2, S4Vectors, IRanges, Seqinfo, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel |
| System Requirements | |
| URL |
See More
| Suggests | testthat, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |