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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software |
| Version | 2.47.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 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 | 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_2.47.0.tar.gz |
| Windows Binary (x86_64) | EDASeq_2.47.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | EDASeq_2.47.0.tgz |
| macOS Binary (sonoma-arm64) | EDASeq_2.47.0.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 |