interactions-package: interactions

In taylo5jm/interactions: Classification of gene expression profile sets generated from combination stimuli

Description

interactions provides functions for classifying gene interaction profiles into mathematically and biologically defined interaction modes and classes, extending the homogenous classes of positive and negative synergies into heterogenous classes comprised of defined interaction modes. This package currently supports transformation of RNA-seq data (expected counts) for classification. limma and edgeR are used extensively for differential expression analysis. topGO is used for gene set enrichment for gene ontology.

Details

Package:	interactions
Type:	Package
Version:	1.0
Date:	2015-08-10
License:	MIT

Author(s)

Justin Taylor Maintainer: Justin Taylor <[e-mail]>

References

Combinatorial code governing cellular responses to complex stimuli http://www.nature.com/ncomms/2015/150421/ncomms/7847/full/ncomms/7847.html voom: precision weights unlock linear model analysis tools for RNA-seq read counts http://statsci.org/smyth/pubs/VoomPreprint.pdf edgeR: a Bioconductor pacakge for differential expression analysis of digital gene expression data http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/ Using transcriptional signatures to assess immune cell function: from basic mechanisms to immune-related disease www.sciencedirect.com/science/article/pii/S0000xxxxx

See Also

~~ Optional links to other man pages, e.g. ~~ ~~ <pkg> ~~

taylo5jm/interactions documentation built on May 31, 2019, 3:57 a.m.