EDASeq

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: Release (3.17)

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>

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

Installation

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

if (!require("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")

EDASeq Vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	DifferentialExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version	2.34.0
In Bioconductor since	BioC 2.9 (R-2.14) (12 years)
License	Artistic-2.0
Depends	Biobase(>= 2.15.1), ShortRead(>= 1.11.42)
Imports	methods, graphics, BiocGenerics, IRanges(>= 1.13.9), aroma.light, Rsamtools(>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager
Linking To
Suggests	BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown
System Requirements
Enhances
URL	https://github.com/drisso/EDASeq
Bug Reports	https://github.com/drisso/EDASeq/issues

Depends On Me	RUVSeq
Imports Me	consensusDE, DaMiRseq, metaseqR2, octad, ribosomeProfilingQC
Suggests Me	awst, bigPint, DEScan2, easyreporting, GRaNIE, HTSFilter, TCGAbiolinks
Links To Me
Build Report

Package Archives

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

Source Package	EDASeq_2.34.0.tar.gz
Windows Binary	EDASeq_2.34.0.zip
macOS Binary (x86_64)	EDASeq_2.34.0.tgz
macOS Binary (arm64)	EDASeq_2.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EDASeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EDASeq
Bioc Package Browser	https://code.bioconductor.org/browse/EDASeq/
Package Short Url	https://bioconductor.org/packages/EDASeq/
Package Downloads Report	Download Stats