Enrichment Approach to Predict Which Transcription Factors are Regulated
performs enrichment analysis
calculates E-value
calculates FDR by Benjamini and Hochberg method
calculates Q-value
calculates Random Control (RC)
calculates TFactS
extracts transcription factor (TF) and target gene (TG) information
calculates Random Control (RC) fastly?
formats the result of enrichment test (ET)
formats the result of Random Control (RC)
TFactSR: A package for identifying critical transcription factors.
R implementation of 'TFactS' to predict which are the transcription factors (TFs), regulated in a biological condition based on lists of differentially expressed genes (DEGs) obtained from transcriptome experiments. This package is based on the 'TFactS' concept by Essaghir et al. (2010) <doi:10.1093/nar/gkq149> and expands it. It allows users to perform 'TFactS'-like enrichment approach. The package can import and use the original catalogue file from the 'TFactS' as well as users' defined catalogues of interest that are not supported by 'TFactS' (e.g., Arabidopsis).