ATACseqTFEA

ATACseqTFEA detects differential activity of transcription factors by analyzing both open region information and transcription factor footprints from ATAC-seq data.

Key Features:

• Differential TF Activity Detection: Identifies changes in transcription factor activity between two conditions.
• Footprint-Based Analysis: Emphasizes differences in transcription factor footprints, specifically cutting sites or insertion sites, in addition to open region information.
• ATAC-seq Integration: Processes genome-wide chromatin accessibility data generated by Tn5 Transposase insertion into open chromatin regions.

Scientific Applications:

• Chromatin Accessibility Analysis: Assesses genome-wide chromatin accessibility patterns from ATAC-seq experiments.
• Transcription Factor Activity Comparison: Broadly evaluates TF activity changes between experimental conditions.

Methodology:

The method improves upon existing computational approaches by incorporating both open region differences and transcription factor footprint differences, specifically cutting sites or insertion sites.