/pipelines

Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data

Primary LanguagePythonMIT LicenseMIT

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