EDASeq

DOI: 10.18129/B9.bioc.EDASeq  

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

HTML R Script EDASeq Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 2.32.0
In Bioconductor since BioC 2.9 (R-2.14) (11.5 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
LinkingTo
Suggests BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown
SystemRequirements
Enhances
URL https://github.com/drisso/EDASeq
BugReports 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_2.32.0.tar.gz
Windows Binary EDASeq_2.32.0.zip
macOS Binary (x86_64) EDASeq_2.32.0.tgz
macOS Binary (arm64) EDASeq_2.32.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: