To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ALDEx2")
In most cases, you don't need to download the package archive at all.
ALDEx2
Analysis of differential abundance taking sample variation into account
Bioconductor version: 3.0
A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.
Author: Greg Gloor, Ruth Grace Wong, Andrew Fernandes, Arianne Albert, Matt Links
Maintainer: Greg Gloor <ggloor at uwo.ca>
Citation (from within R,
enter citation("ALDEx2")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ALDEx2")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ALDEx2")
| R Script | An R Package for determining differential abundance in high throughput sequencing experiments | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | file LICENSE |
| Depends | methods |
| Imports | GenomicRanges |
| LinkingTo | |
| Suggests | parallel, BiocParallel |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ALDEx2_1.0.0.tar.gz |
| Windows Binary | ALDEx2_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | ALDEx2_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | ALDEx2_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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