Repositories list

• Flynn_WGS_Analysis

  Public
  This repo stores code that performs variant analysis and chromothripsis detection on PDX WGS data.

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

• beffert_ho_lab_pacbio_ad_pilot

  Public
  A reproducible and modular pipeline for processing PacBio IsoSeq long-read RNA sequencing data using Nextflow. Supports transcript quantification, splicing analysis, and differential expression analyses.

  HTML

  •

  MIT License

  •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

• MG_AD_scATAC

  Public
  A pipeline for integrating snATAC-seq and snRNA-seq data to uncover regulatory mechanisms underlying microglial state transitions in Alzheimer’s disease.

  R

  •

  MIT License

  •1•2•0•0•Updated Sep 16, 2025Sep 16, 2025

• Single_Cell_Cross-Species_Integration_Algorithm

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 27, 2025Aug 27, 2025

• ChIPSeq_GPS2_CTCF_PerissiLab

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

• White_sTF_PROseq

  Public
  BMSIP project in Khalil lab for measuring synthetic transcription factor kinetics with PROseq

  Python

  •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

• p_simiae_tn_seq_automated_gap_fill

  Public
  MIT License

  •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

• Psimiae_API_Melisa_Ilija_BMSIP_2025

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

• Chen_lab_BMSIP_25

  Public
  MIT License

  •0•0•0•0•Updated Jun 4, 2025Jun 4, 2025

• DriesLab_spatial-engraftomics

  Public
  MIT License

  •0•0•0•0•Updated May 30, 2025May 30, 2025

• MMG

  Public
  R

  •1•0•0•0•Updated Mar 21, 2025Mar 21, 2025

• Zeldich_DS_scRNAseq

  Public
  MIT License

  •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024