suwangbio/beta repository overview

Summary Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor’s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor’s activating or repressive function. Here we describe the implementation and features of BETA to demonstrate its application to several datasets. BETA requires ~2GB RAM and 1h for the whole procedure.

Introduction BETA is a free software to do Transcription Factor and Chromatin Regulator target analysis. Three subcommands of BETA make it user-friendly.

BETA basic: TF activating and repressive function prediction and direct targets detecting. BETA plus: TF activating and repressive function prediction, direct targets detecting and motif analysis on target regions. BETA minus: TF target genes prediction based on the regulatory potential score with only binding data.

CITATION

Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., ... & Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515.

PMID: 24263090