EDASeq

DOI: 10.18129/B9.bioc.EDASeq    

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: Release (3.11)

Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

Author: Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Ludwig Geistlinger [ctb]

Maintainer: Davide Risso <risso.davide 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("EDASeq")

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("EDASeq")

 

HTML	R Script	EDASeq Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version	2.22.0
In Bioconductor since	BioC 2.9 (R-2.14) (9 years)
License	Artistic-2.0
Depends	Biobase(>= 2.15.1), ShortRead(>= 1.11.42)
Imports	methods, graphics, BiocGenerics, IRanges(>= 1.13.9), DESeq, aroma.light, Rsamtools(>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager
LinkingTo
Suggests	BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat
SystemRequirements
Enhances
URL	https://github.com/drisso/EDASeq
BugReports	https://github.com/drisso/EDASeq/issues
Depends On Me	metaseqR, RUVSeq
Imports Me	consensusDE, DaMiRseq, metaseqR2, ribosomeProfilingQC
Suggests Me	bigPint, DEScan2, easyreporting, HTSFilter, TCGAbiolinks
Links To Me
Build Report

Package Archives

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

Source Package	EDASeq_2.22.0.tar.gz
Windows Binary	EDASeq_2.22.0.zip
macOS 10.13 (High Sierra)	EDASeq_2.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EDASeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EDASeq
Package Short Url	https://bioconductor.org/packages/EDASeq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive