EDASeq
Exploratory Data Analysis and Normalization for RNA-Seq
Bioconductor version: Release (3.20)
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("EDASeq")):
Installation
To install this package, start R (version "4.4") 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")| EDASeq Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software |
| Version | 2.40.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (13 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.
| Source Package | EDASeq_2.40.0.tar.gz |
| Windows Binary (x86_64) | EDASeq_2.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | EDASeq_2.40.0.tgz |
| macOS Binary (arm64) | EDASeq_2.40.0.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 |