chromVAR

chromVAR analyzes sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases.

Key Features:

• Motif and Annotation-Based Variation Analysis: Determines variation in chromatin accessibility across sets of annotations or peaks sharing the same motif.
• Technical Bias Control: Controls for technical biases in sparse chromatin accessibility data.
• Clustering of scATAC-seq Profiles: Enables accurate clustering of single-cell ATAC-seq profiles.
• Sequence Motif Characterization: Characterizes known and de novo sequence motifs associated with variation in chromatin accessibility.

Scientific Applications:

• Single-Cell Epigenomic Analysis: Analyzes scATAC-seq data where conventional analysis is challenging due to sparsity.
• Sparse Bulk ATAC-seq Analysis: Processes sparse bulk ATAC-seq experiments.
• DNase-seq Analysis: Handles sparse DNase-seq experiments.
• Transcription Factor Association Inference: Infers transcription-factor-associated accessibility from single-cell epigenomic data.

Methodology:

chromVAR estimates gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases.