GenoGAM

DOI: 10.18129/B9.bioc.GenoGAM    

A GAM based framework for analysis of ChIP-Seq data

Bioconductor version: Release (3.6)

This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package 'mgcv'. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Estimation of dispersion and smoothing parameters is performed by cross-validation. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.

Author: Georg Stricker [aut, cre], Alexander Engelhardt [aut], Julien Gagneur [aut]

Maintainer: Georg Stricker <georg.stricker at in.tum.de>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenoGAM")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenoGAM")

 

PDF	R Script	GenoGAM: Genome-wide generalized additive models
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, DifferentialExpression, DifferentialPeakCalling, Epigenetics, Genetics, Regression, Software
Version	1.6.0
In Bioconductor since	BioC 3.3 (R-3.3) (2 years)
License	GPL-2
Depends	R (>= 3.3), Rsamtools(>= 1.18.2), SummarizedExperiment(>= 1.1.19), GenomicRanges(>= 1.29.14), methods
Imports	BiocParallel(>= 1.5.17), data.table (>= 1.9.4), DESeq2(>= 1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb(>= 1.7.6), GenomicAlignments(>= 1.7.17), IRanges(>= 2.11.16), mgcv (>= 1.8), reshape2 (>= 1.4.1), S4Vectors(>= 0.9.34), Biostrings(>= 2.39.14)
LinkingTo
Suggests	BiocStyle, chipseq(>= 1.21.2), LSD (>= 3.0.0), genefilter(>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr
SystemRequirements
Enhances
URL	https://github.com/gstricker/GenoGAM
BugReports	https://github.com/gstricker/GenoGAM/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	GenoGAM_1.6.0.tar.gz
Windows Binary	GenoGAM_1.6.0.zip
Mac OS X 10.11 (El Capitan)	GenoGAM_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenoGAM
Package Short Url	http://bioconductor.org/packages/GenoGAM/
Package Downloads Report	Download Stats