This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see EDASeq.
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")
):
To install this package, start R (version "3.5") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EDASeq")
HTML | R Script | EDASeq Vignette |
Reference Manual | ||
Text | NEWS |
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 |
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, EnrichmentBrowser, TCGAbiolinks |
Suggests Me | DEScan2, HTSFilter |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
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/ |
Package Downloads Report | Download Stats |
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