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EDASeq

This is the development version of EDASeq; for the stable release version, see EDASeq.

Exploratory Data Analysis and Normalization for RNA-Seq


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.37.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
System Requirements
URL https://github.com/drisso/EDASeq
Bug Reports https://github.com/drisso/EDASeq/issues
See More
Suggests BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown
Linking To
Enhances
Depends On Me RUVSeq
Imports Me consensusDE, DaMiRseq, metaseqR2, octad, ribosomeProfilingQC
Suggests Me awst, DEScan2, easyreporting, GRaNIE, HTSFilter, TCGAbiolinks
Links To Me
Build Report Build Report

Package Archives

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

Source Package EDASeq_2.37.0.tar.gz
Windows Binary EDASeq_2.37.0.zip (64-bit only)
macOS Binary (x86_64) EDASeq_2.37.0.tgz
macOS Binary (arm64) EDASeq_2.37.0.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