Repositories list

• ims_docker

  Public
  Python

  •

  MIT License

  •1•0•1•2•Updated Oct 24, 2024Oct 24, 2024

• pipeline-chromatin-accessibility

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

  genomicsdata-analysisatac-seq+ 3epigenomicschromatin-accessibiityatac-seq-pipeline

  Python

  •

  MIT License

  •0•1•0•0•Updated Jun 21, 2024Jun 21, 2024

• RepeatEnrichment

  Public
  Repeat enrichment analysis

  R

  •0•1•0•0•Updated Apr 23, 2024Apr 23, 2024

• MEMOS

  Public
  Mutation Enrichment of Motifs

  R

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Nov 15, 2023Nov 15, 2023

• DUnCAN_issues

  Public
  To record bugs on DuNCAN

  0•0•0•0•Updated Oct 2, 2023Oct 2, 2023

• CoBE_encode_ChIP-seq_pipeline

  Public
  Shell

  •0•0•0•0•Updated Mar 27, 2023Mar 27, 2023

• 3d-reorganization-prostate-cancer

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

  bioinformatics3d-genomeprostate-cancer+ 1structural-variants

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 8, 2023Mar 8, 2023

• scMultiome

  Public
  From Shalini Bahl

  R

  •0•0•0•0•Updated Nov 11, 2022Nov 11, 2022

• CUT-RUN

  Public
  Shell

  •0•0•0•0•Updated Oct 5, 2022Oct 5, 2022

• cap-tcr

  Public
  cap-tcr

  Python

  •1•0•0•0•Updated Jul 7, 2022Jul 7, 2022

• CoBE

  Public
  code for executables on HPC

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 2, 2022Mar 2, 2022

• CoBE_encode_ATAC_pipeline

  Public
  0•0•0•0•Updated Feb 9, 2022Feb 9, 2022

• kallisto_snakemake

  Public
  Python

  •0•0•0•0•Updated Feb 9, 2022Feb 9, 2022

• cellranger-on-h4h

  Public
  0•0•0•0•Updated Feb 9, 2022Feb 9, 2022

• run_encode_ATAC_pipeline

  Public
  0•0•0•0•Updated Mar 9, 2021Mar 9, 2021

• singularity_cellranger

  Public
  singularity container for 10X data processing

  MIT License

  •1•0•0•0•Updated May 14, 2020May 14, 2020

• gencode-annotations

  Public
  Pre-processing of the GENCODE human genome annotation

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 10, 2020Mar 10, 2020

• Zhou_FOXA1_ncomm_2020

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

  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 24, 2020Jan 24, 2020

• pipeline-bisulfite-sequencing

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

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 17, 2020Jan 17, 2020

• SMURF

  Public
  Significantly Mutated Region Finder

  R

  •

  GNU General Public License v3.0

  •1•6•1•0•Updated Jan 11, 2019Jan 11, 2019

• C3D

  Public
  Cross Cell-type Correlation in DNaseI hypersensitivity

  Shell

  •

  GNU General Public License v3.0

  •6•0•0•0•Updated Aug 27, 2018Aug 27, 2018

• VSE

  Public
  Varient Set Enrichment

  Perl

  •3•0•0•0•Updated Aug 1, 2017Aug 1, 2017

• ABC

  Public
  Allele-specific Binding from Chip-seq

  Perl

  •10•0•0•0•Updated Aug 1, 2017Aug 1, 2017