Repositories list

• dominoSignal

  Public
  A software package for connecting cell level features in single cell RNA sequencing data with receptor ligand activity.

  R

  •

  GNU General Public License v3.0

  •77 forks•66 stars•1616 issues•11 pull request•Updated Apr 17, 2026Apr 17, 2026

• staple-paper

  Public
  brain dataset analysis

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• ontrack

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• dpt-paper-2026

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 3, 2026Mar 3, 2026

• Differential_Cell_Signaling_Test

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 17, 2026Feb 17, 2026

• spatial-test

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 12, 2025Dec 12, 2025

• fertiglab.github.io

  Public
  SCSS

  •11 fork•00 stars•11 issue•00 pull requests•Updated Oct 19, 2025Oct 19, 2025

• CoGAPS

  Public
  Bayesian MCMC matrix factorization algorithm

  machine-learningbioinformaticsbayesian-inference+ 3

  machine-learningbioinformaticsbayesian-inferencesingle-cell-rna-seqnon-negative-matrix-factorizationhuman-cell-atlas

  C++

  •

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

  •1616 forks•7171 stars•2525 issues•11 pull request•Updated Sep 19, 2025Sep 19, 2025

• dpt-combined-analysis

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 11, 2025Sep 11, 2025

• Spatial_Venous_Invasion_PDAC

  Public
  Spatial profiling of venous invasion in human pancreatic ductal adenocarcinoma

  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 19, 2025Aug 19, 2025

• btc-spatial-pipelines

  Public
  Nextflow spatial pipelines (for Spatial Transcriptomics, IMC, etc.)

  Nextflow

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 30, 2025Jun 30, 2025

• pycogaps

  Public
  python API to the CoGAPS NMF package

  Python

  •

  GNU General Public License v2.0

  •77 forks•2121 stars•2121 issues•11 pull request•Updated May 19, 2025May 19, 2025

• Homolig

  Public
  Homolig is a series of tools designed to compare the physiotypic properties of TCR and BCRs. Created by Alexander Girgis, Emily Davis-Marcisak, and Theron Palme…

  C++

  •

  GNU Affero General Public License v3.0

  •11 fork•00 stars•11 issue•11 pull request•Updated May 12, 2025May 12, 2025

• Human_PanIN_Spatial_Analysis

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 7, 2025May 7, 2025

• J1798_trial_paper

  Public
  scripts for the J1798 trial paper

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2025Mar 19, 2025

• J15221_trial_paper

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2025Mar 19, 2025

• dpt-visium-notebook

  Public
  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 10, 2025Mar 10, 2025

• onboarding

  Public
  Ruby

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 10, 2025Feb 10, 2025

• bayestme

  Public
  BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data

  Jupyter Notebook

  •

  Other

  •44 forks•00 stars•00 issues•00 pull requests•Updated Feb 4, 2025Feb 4, 2025

• spatial-pipeline

  Public
  Nextflow

  •00 forks•00 stars•77 issues•00 pull requests•Updated Nov 22, 2024Nov 22, 2024

• HCCTLS

  Public
  R

  •22 forks•22 stars•00 issues•00 pull requests•Updated Nov 15, 2024Nov 15, 2024

• prgpmf

  Public
  Poisson-randomized gamma Poisson matrix factorization

  Python

  •33 forks•00 stars•00 issues•00 pull requests•Updated Nov 2, 2024Nov 2, 2024

• ATACCoGAPS

  Public
  R

  •11 fork•44 stars•00 issues•00 pull requests•Updated Oct 22, 2024Oct 22, 2024

• actions

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Aug 12, 2024Aug 12, 2024

• splicemutr

  Public
  R

  •

  GNU General Public License v3.0

  •11 fork•77 stars•00 issues•00 pull requests•Updated Jul 5, 2024Jul 5, 2024

• hypoxiaROSanalysis

  Public
  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 3, 2024Jul 3, 2024

• PanIN_carcinogeneisis_spatial_analysis

  Public
  HTML

  •

  GNU General Public License v3.0

  •11 fork•00 stars•11 issue•00 pull requests•Updated Jun 4, 2024Jun 4, 2024

• mKRAS-Vax

  Public
  scRNA and TCR analysis, including T-cell expansion assays, from subjects in J1994 manuscript by Huff et al.

  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 20, 2024May 20, 2024

• nf-bin-test

  Public
  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 16, 2024May 16, 2024

• nfcore-modules

  Public
  Repository to host tool-specific module files for the Nextflow DSL2 community!

  Nextflow

  •

  MIT License

  •1k1k forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2024Apr 30, 2024