Repositories list

• whereAreECDNAs

  Public

  LupienLab/whereAreECDNAs’s past year of commit activity
  R

  •

  MIT License

  •00 forks in LupienLab/whereAreECDNAs•00 stars in LupienLab/whereAreECDNAs•00 issues in LupienLab/whereAreECDNAs•00 pull requests in LupienLab/whereAreECDNAs•Updated Sep 4, 2026Sep 4, 2026

• ims_docker

  Public
  Python

  •

  MIT License

  •11 fork in LupienLab/ims_docker•00 stars in LupienLab/ims_docker•77 issues in LupienLab/ims_docker•22 pull requests in LupienLab/ims_docker•Updated Jul 25, 2026Jul 25, 2026

• ecDNA_in_GBM

  Public

  LupienLab/ecDNA_in_GBM’s past year of commit activity
  R

  •00 forks in LupienLab/ecDNA_in_GBM•00 stars in LupienLab/ecDNA_in_GBM•00 issues in LupienLab/ecDNA_in_GBM•00 pull requests in LupienLab/ecDNA_in_GBM•Updated Jul 19, 2026Jul 19, 2026

• .github

  Public

  LupienLab/.github’s past year of commit activity
  00 forks in LupienLab/.github•00 stars in LupienLab/.github•00 issues in LupienLab/.github•00 pull requests in LupienLab/.github•Updated Dec 9, 2025Dec 9, 2025

• scMultiomePCa

  Public
  R

  •11 fork in LupienLab/scMultiomePCa•00 stars in LupienLab/scMultiomePCa•00 issues in LupienLab/scMultiomePCa•00 pull requests in LupienLab/scMultiomePCa•Updated Aug 14, 2025Aug 14, 2025

• runLola

  Public

  LupienLab/runLola’s past year of commit activity
  Shell

  •00 forks in LupienLab/runLola•00 stars in LupienLab/runLola•00 issues in LupienLab/runLola•00 pull requests in LupienLab/runLola•Updated May 28, 2025May 28, 2025

• consensus_ATAC

  Public

  LupienLab/consensus_ATAC’s past year of commit activity
  R

  •00 forks in LupienLab/consensus_ATAC•00 stars in LupienLab/consensus_ATAC•00 issues in LupienLab/consensus_ATAC•00 pull requests in LupienLab/consensus_ATAC•Updated May 28, 2025May 28, 2025

• pipeline-chromatin-accessibility

  Public

  LupienLab/pipeline-chromatin-accessibility’s past year of commit activity
  Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)

  genomicsdata-analysisatac-seq+ 3

  genomicsdata-analysisatac-seqepigenomicschromatin-accessibiityatac-seq-pipeline

  Python

  •

  MIT License

  •00 forks in LupienLab/pipeline-chromatin-accessibility•11 star in LupienLab/pipeline-chromatin-accessibility•00 issues in LupienLab/pipeline-chromatin-accessibility•00 pull requests in LupienLab/pipeline-chromatin-accessibility•Updated Apr 29, 2025Apr 29, 2025

• RepeatEnrichment

  Public

  LupienLab/RepeatEnrichment’s past year of commit activity
  Repeat enrichment analysis

  R

  •00 forks in LupienLab/RepeatEnrichment•11 star in LupienLab/RepeatEnrichment•00 issues in LupienLab/RepeatEnrichment•00 pull requests in LupienLab/RepeatEnrichment•Updated Apr 23, 2024Apr 23, 2024

• MEMOS

  Public

  LupienLab/MEMOS’s past year of commit activity
  Mutation Enrichment of Motifs

  R

  •

  GNU General Public License v3.0

  •00 forks in LupienLab/MEMOS•22 stars in LupienLab/MEMOS•00 issues in LupienLab/MEMOS•00 pull requests in LupienLab/MEMOS•Updated Nov 15, 2023Nov 15, 2023

• DUnCAN_issues

  Public
  To record bugs on DuNCAN

  00 forks in LupienLab/DUnCAN_issues•00 stars in LupienLab/DUnCAN_issues•00 issues in LupienLab/DUnCAN_issues•00 pull requests in LupienLab/DUnCAN_issues•Updated Oct 2, 2023Oct 2, 2023

• CoBE_encode_ChIP-seq_pipeline

  Public
  Shell

  •00 forks in LupienLab/CoBE_encode_ChIP-seq_pipeline•00 stars in LupienLab/CoBE_encode_ChIP-seq_pipeline•00 issues in LupienLab/CoBE_encode_ChIP-seq_pipeline•00 pull requests in LupienLab/CoBE_encode_ChIP-seq_pipeline•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+ 1

  bioinformatics3d-genomeprostate-cancerstructural-variants

  HTML

  •

  GNU General Public License v3.0

  •00 forks in LupienLab/3d-reorganization-prostate-cancer•00 stars in LupienLab/3d-reorganization-prostate-cancer•00 issues in LupienLab/3d-reorganization-prostate-cancer•00 pull requests in LupienLab/3d-reorganization-prostate-cancer•Updated Mar 8, 2023Mar 8, 2023

• scMultiome

  Public
  From Shalini Bahl

  R

  •00 forks in LupienLab/scMultiome•00 stars in LupienLab/scMultiome•00 issues in LupienLab/scMultiome•00 pull requests in LupienLab/scMultiome•Updated Nov 11, 2022Nov 11, 2022

• CUT-RUN

  Public
  Shell

  •00 forks in LupienLab/CUT-RUN•00 stars in LupienLab/CUT-RUN•00 issues in LupienLab/CUT-RUN•00 pull requests in LupienLab/CUT-RUN•Updated Oct 5, 2022Oct 5, 2022

• cap-tcr

  Public
  cap-tcr

  Python

  •11 fork in LupienLab/cap-tcr•00 stars in LupienLab/cap-tcr•00 issues in LupienLab/cap-tcr•00 pull requests in LupienLab/cap-tcr•Updated Jul 7, 2022Jul 7, 2022

• CoBE

  Public
  code for executables on HPC

  Shell

  •

  Apache License 2.0

  •00 forks in LupienLab/CoBE•00 stars in LupienLab/CoBE•00 issues in LupienLab/CoBE•00 pull requests in LupienLab/CoBE•Updated Mar 2, 2022Mar 2, 2022

• CoBE_encode_ATAC_pipeline

  Public
  00 forks in LupienLab/CoBE_encode_ATAC_pipeline•00 stars in LupienLab/CoBE_encode_ATAC_pipeline•00 issues in LupienLab/CoBE_encode_ATAC_pipeline•00 pull requests in LupienLab/CoBE_encode_ATAC_pipeline•Updated Feb 9, 2022Feb 9, 2022

• kallisto_snakemake

  Public
  Python

  •00 forks in LupienLab/kallisto_snakemake•00 stars in LupienLab/kallisto_snakemake•00 issues in LupienLab/kallisto_snakemake•00 pull requests in LupienLab/kallisto_snakemake•Updated Feb 9, 2022Feb 9, 2022

• cellranger-on-h4h

  Public
  00 forks in LupienLab/cellranger-on-h4h•00 stars in LupienLab/cellranger-on-h4h•00 issues in LupienLab/cellranger-on-h4h•00 pull requests in LupienLab/cellranger-on-h4h•Updated Feb 9, 2022Feb 9, 2022

• run_encode_ATAC_pipeline

  Public
  00 forks in LupienLab/run_encode_ATAC_pipeline•00 stars in LupienLab/run_encode_ATAC_pipeline•00 issues in LupienLab/run_encode_ATAC_pipeline•00 pull requests in LupienLab/run_encode_ATAC_pipeline•Updated Mar 9, 2021Mar 9, 2021

• singularity_cellranger

  Public
  singularity container for 10X data processing

  MIT License

  •11 fork in LupienLab/singularity_cellranger•00 stars in LupienLab/singularity_cellranger•00 issues in LupienLab/singularity_cellranger•00 pull requests in LupienLab/singularity_cellranger•Updated May 14, 2020May 14, 2020

• gencode-annotations

  Public
  Pre-processing of the GENCODE human genome annotation

  Python

  •

  MIT License

  •00 forks in LupienLab/gencode-annotations•00 stars in LupienLab/gencode-annotations•00 issues in LupienLab/gencode-annotations•00 pull requests in LupienLab/gencode-annotations•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

  •00 forks in LupienLab/Zhou_FOXA1_ncomm_2020•11 star in LupienLab/Zhou_FOXA1_ncomm_2020•00 issues in LupienLab/Zhou_FOXA1_ncomm_2020•00 pull requests in LupienLab/Zhou_FOXA1_ncomm_2020•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

  •00 forks in LupienLab/pipeline-bisulfite-sequencing•00 stars in LupienLab/pipeline-bisulfite-sequencing•00 issues in LupienLab/pipeline-bisulfite-sequencing•00 pull requests in LupienLab/pipeline-bisulfite-sequencing•Updated Jan 17, 2020Jan 17, 2020

• SMURF

  Public
  Significantly Mutated Region Finder

  R

  •

  GNU General Public License v3.0

  •11 fork in LupienLab/SMURF•77 stars in LupienLab/SMURF•11 issue in LupienLab/SMURF•00 pull requests in LupienLab/SMURF•Updated Jan 11, 2019Jan 11, 2019

• C3D

  Public
  Cross Cell-type Correlation in DNaseI hypersensitivity

  Shell

  •

  GNU General Public License v3.0

  •66 forks in LupienLab/C3D•00 stars in LupienLab/C3D•00 issues in LupienLab/C3D•00 pull requests in LupienLab/C3D•Updated Aug 27, 2018Aug 27, 2018

• VSE

  Public
  Varient Set Enrichment

  Perl

  •33 forks in LupienLab/VSE•00 stars in LupienLab/VSE•00 issues in LupienLab/VSE•00 pull requests in LupienLab/VSE•Updated Aug 1, 2017Aug 1, 2017

• ABC

  Public
  Allele-specific Binding from Chip-seq

  Perl

  •1010 forks in LupienLab/ABC•00 stars in LupienLab/ABC•00 issues in LupienLab/ABC•00 pull requests in LupienLab/ABC•Updated Aug 1, 2017Aug 1, 2017