LupienLab

SMURF

Significantly Mutated Region Finder

MEMOS

Mutation Enrichment of Motifs

pipeline-chromatin-accessibility

Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)

Zhou_FOXA1_ncomm_2020

Plots, code, and analyses for Zhou et al, Nature Communications, 2020

3d-reorganization-prostate-cancer

Code, analysis, and results for Hawley, Zhou, et al., Cancer Research, 2021.

ABC

Allele-specific Binding from Chip-seq

cap-tcr

cap-tcr

CUT-RUN

gencode-annotations

Pre-processing of the GENCODE human genome annotation

kallisto_snakemake

scMultiome

From Shalini Bahl

VSE

Varient Set Enrichment

C3D

Cross Cell-type Correlation in DNaseI hypersensitivity

cellranger-on-h4h

CoBE

code for executables on HPC

CoBE_encode_ATAC_pipeline

CoBE_encode_ChIP-seq_pipeline

DUnCAN_issues

To record bugs on DuNCAN

ims_docker

pipeline-bisulfite-sequencing

Instructions on how to perform bisulfite sequencing data pre-processing and analyses

singularity_cellranger

singularity container for 10X data processing