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Bioconductor - EDASeq (development version)

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 (3.22)

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 "4.5") 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")

Details biocViews DifferentialExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software Version 2.43.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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, MOSClip, TCGAbiolinks Links To Me Build Report Build Report Package Archives

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

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