Repositories list

• sopa

  Public
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •45•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• parallax

  Public
  Nextflow

  •

  MIT License

  •1•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• prep-sopa

  Public
  Python

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• images

  Public
  development images for bioinformatics

  Dockerfile

  •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

• morrison-2026

  Public
  0•0•0•0•Updated Jan 12, 2026Jan 12, 2026

• lit-report

  Public
  Python

  •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

• hubmap-xenium-submitter

  Public
  Python

  •0•0•0•0•Updated Sep 11, 2025Sep 11, 2025

• coreSC

  Public
  A wrapper to execute the core functions of the Seurat pipeline.

  R

  •

  MIT License

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• jobs

  Public
  Template hpc batch scripts

  Python

  •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• lazy-slide-pilot

  Public
  0•0•0•0•Updated Jul 24, 2025Jul 24, 2025

• xenium-explorer-files

  Public
  JavaScript

  •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

• scdownstream

  Public
  A single cell transcriptomics pipeline for QC, integration and making the data presentable

  Nextflow

  •

  MIT License

  •61•0•0•0•Updated Jul 18, 2025Jul 18, 2025

• nf-core-resolvinf-demo

  Public
  Nextflow

  •

  MIT License

  •1•0•0•0•Updated Jun 10, 2025Jun 10, 2025

• utils

  Public
  0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

• corescpy

  Public
  A wrapper to simplify the execution of Single Cell analysis with the sc verse

  Python

  •

  Other

  •0•5•4•0•Updated Oct 7, 2024Oct 7, 2024

• docs

  Public
  Documentation for the Cho Lab

  0•3•0•0•Updated Oct 4, 2024Oct 4, 2024

• levantovsky-2024

  Public
  Published code and computational methods for Levantovsky et. al. 2024

  Jupyter Notebook

  •3•1•0•0•Updated Aug 15, 2024Aug 15, 2024

• chobiolab.org

  Public
  TeX

  •

  MIT License

  •0•0•0•0•Updated Jul 2, 2024Jul 2, 2024

• tech-exam-answers

  Public
  Technical exam for dry lab roles

  HTML

  •3•0•0•0•Updated Apr 29, 2024Apr 29, 2024

• tech-exam

  Public
  Technical exam for dry lab roles

  HTML

  •3•0•0•0•Updated Apr 29, 2024Apr 29, 2024

• segpro

  Public
  Post-run cell segmentation using Cellpose

  Python

  •0•0•0•0•Updated Mar 21, 2024Mar 21, 2024

• sc-metadata

  Public
  Management of the single cell metadatabase REDCap project.

  Jupyter Notebook

  •0•0•0•0•Updated Dec 4, 2023Dec 4, 2023

• temPlot

  Public
  A collection of useful plotting template functions

  0•0•5•0•Updated Aug 23, 2023Aug 23, 2023

• annotation

  Public
  A wrapper to execute the CellTypist automated annotation method with Seurat objects.

  R

  •0•1•0•0•Updated Jul 13, 2023Jul 13, 2023

• velocity

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jul 7, 2023Jul 7, 2023

• devenvs

  Public
  Development environments

  Dockerfile

  •0•0•0•0•Updated Apr 11, 2023Apr 11, 2023

• configs

  Public
  Config files used to define parameters specific to compute environments at different Institutions

  Nextflow

  •

  MIT License

  •348•0•0•0•Updated Feb 22, 2023Feb 22, 2023

• tools

  Public archive
  A collection of containerized bioinformatic tools

  Dockerfile

  •0•0•0•0•Updated Dec 19, 2022Dec 19, 2022

• gitops-qa

  Public
  HTML

  •

  Apache License 2.0

  •6•0•0•0•Updated Feb 17, 2022Feb 17, 2022

• Scripts_Nayar_et_al_Nature_2021

  Public
  Codes used to generate figures for Nayar et al., manuscript

  R

  •0•0•0•0•Updated Mar 22, 2021Mar 22, 2021