DOI: 10.18129/B9.bioc.EDASeq    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see EDASeq.

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: 3.8

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")):


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biocViews DifferentialExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 2.16.3
In Bioconductor since BioC 2.9 (R-2.14) (7.5 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
Suggests BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat
URL https://github.com/drisso/EDASeq
BugReports https://github.com/drisso/EDASeq/issues
Depends On Me metaseqR, RUVSeq
Imports Me consensusDE, DaMiRseq, EnrichmentBrowser, TCGAbiolinks
Suggests Me DEScan2, HTSFilter
Links To Me
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Source Package EDASeq_2.16.3.tar.gz
Windows Binary EDASeq_2.16.3.zip
Mac OS X 10.11 (El Capitan) EDASeq_2.16.3.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 http://bioconductor.org/packages/EDASeq/
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