betterChromVAR

betterChromVAR implements a much faster analytical version of chromVAR with additional features to infer transcription factor activity from bulk or single-cell ATAC-seq data using motif annotations or binding probabilities.

Key Features:

• Accelerated chromVAR implementation: Provides a substantially faster analytical implementation of the chromVAR algorithm for computing transcription factor activity scores.
• Multi-modal input support: Processes both bulk and single-cell ATAC-seq data for transcription factor activity inference.
• Flexible annotation inputs: Accepts motif annotations or binding probabilities as input for transcription factor activity estimation.
• CVnorm normalization: Includes the CVnorm normalization method based on chromVAR logic for data normalization.

Scientific Applications:

• Transcription factor activity inference: Identifies active transcription factors from chromatin accessibility profiles in bulk or single-cell ATAC-seq experiments.
• Chromatin variation analysis: Quantifies variation in chromatin accessibility across genomic regions to understand regulatory heterogeneity.

Methodology:

The tool employs an analytical implementation of the chromVAR algorithm with CVnorm normalization based on chromVAR logic.