recipe bioconductor-bridge

Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/bridge.html

License

GPL (>= 2)

Recipe

/bioconductor-bridge/meta.yaml

Links

biotools: bridge, doi: 10.1111/j.1541-0420.2005.00397.x

package bioconductor-bridge

(downloads) docker_bioconductor-bridge

Versions

1.48.0-1, 1.48.0-0, 1.46.0-0, 1.44.0-0, 1.42.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-bridge

and update with:

conda update bioconductor-bridge

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-bridge:<tag>

(see bioconductor-bridge/tags for valid values for <tag>)