To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("BADER")
In most cases, you don't need to download the package archive at all.
BADER
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bioconductor version: 3.0
For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.
Author: Andreas Neudecker, Matthias Katzfuss
Maintainer: Andreas Neudecker <a.neudecker at arcor.de>
Citation (from within R,
enter citation("BADER")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("BADER")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BADER")
| R Script | Analysing RNA-Seq data with the "BADER" package | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, RNASeq, SAGE, Sequencing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-2 |
| Depends | |
| Imports | |
| LinkingTo | |
| Suggests | pasilla(>= 0.2.10) |
| 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 | BADER_1.4.0.tar.gz |
| Windows Binary | BADER_1.4.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | BADER_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | BADER_1.4.0.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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