analytical tools

Analytical tools and pipelines developed by the Gaulton Lab at UCSD.

bulk_ATAC-seq

Process bulk ATAC-seq data.

Last update: 08/30/2017
Maintained by: Josh Chiou

snATAC-seq

Process and analyze single nucleus ATAC-seq data.

Last update: 12/10/2018
Maintained by: Josh Chiou

rare_variants

Rare variant testing in disrupted footprints.

Last update: 06/26/2017
Maintained by: Josh Chiou

reweight_variants

Re-weighting variants after applying epigenetic and eQTL priors.

Last update: 07/02/2017
Maintained by: Josh Chiou

ATAC-seq_footprinting

Footprinting in ATAC-seq peaks.

Last update: 06/11/2017
Maintained by: Josh Chiou

ChIP-seq

ChIP-seq data

Last update: 07/21/2017
Maintained by: Josh Chiou

variant_annotation_matrix

Binary variant-by-annotaiton matrices.

Last update: 06/27/2017
Maintained by: Anthony Aylward

fgwas_workflow

Implementation of the workflow suggested by the FGWAS manual.

Last update: 08/10/2017
Maintained by: Anthony Aylward

ChIP-seq_imbalance

Allelic imbalance analysis and workflow for ChIP-seq data.

Last update: 09/7/2018
Maintained by: Anthony Aylward

infer_footprints

Infer TF binding footprints from DNase-seq data.

Last update: 09/24/2017
Maintained by: Mei-Lin Okino, Anthony Aylward