gfold - Generalized fold change for ranking differentially expressed genes from RNA-seq data.
GFOLD is especially useful when no replicate is available. GFOLD generalizes the fold change by considering the posterior distribution of log fold change, such that each gene is assigned a reliable fold change. It overcomes the shortcoming of p-value that measures the significance of whether a gene is differentially expressed under different conditions instead of measuring relative expression changes, which are more interesting in many studies. It also overcomes the shortcoming of fold change that suffers from the fact that the fold change of genes with low read count are not so reliable as that of genes with high read count, even these two genes show the same fold change.
module spider gfold to find out what environment modules are available for this application.
- HPC_GFOLD_DIR - installation directory
- HPC_GFOLD_BIN - executable directory
If you publish research that uses gfold you have to cite it as follows:
Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics 2012