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

  •7•4•3•4•Updated Jan 22, 2025Jan 22, 2025

• onboarding

  Public
  Ruby

  •

  MIT License

  •0•0•1•1•Updated Jan 21, 2025Jan 21, 2025

• CoGAPS

  Public
  Bayesian MCMC matrix factorization algorithm

  machine-learningbioinformaticsbayesian-inference+ 3single-cell-rna-seqnon-negative-matrix-factorizationhuman-cell-atlas

  C++

  •

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

  •17•66•24•2•Updated Jan 21, 2025Jan 21, 2025

• fertiglab.github.io

  Public
  SCSS

  •1•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• spatial-pipeline

  Public
  Nextflow

  •0•0•7•0•Updated Nov 22, 2024Nov 22, 2024

• HCCTLS

  Public
  R

  •1•1•0•0•Updated Nov 15, 2024Nov 15, 2024

• prgpmf

  Public
  Poisson-randomized gamma Poisson matrix factorization

  Python

  •3•0•0•0•Updated Nov 2, 2024Nov 2, 2024

• 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 Palmer.

  C++

  •

  GNU Affero General Public License v3.0

  •1•0•1•1•Updated Nov 1, 2024Nov 1, 2024

• ATACCoGAPS

  Public
  R

  •1•4•0•0•Updated Oct 22, 2024Oct 22, 2024

• actions

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•1•0•Updated Aug 12, 2024Aug 12, 2024

• J1798_trial_paper

  Public
  scripts for the J1798 trial paper

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

• splicemutr

  Public
  R

  •

  GNU General Public License v3.0

  •1•5•0•0•Updated Jul 5, 2024Jul 5, 2024

• hypoxiaROSanalysis

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Jul 3, 2024Jul 3, 2024

• PanIN_carcinogeneisis_spatial_analysis

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•1•0•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

  •0•0•0•0•Updated May 20, 2024May 20, 2024

• nf-bin-test

  Public
  Nextflow

  •0•0•0•0•Updated May 16, 2024May 16, 2024

• nfcore-modules

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

  Nextflow

  •

  MIT License

  •743•0•0•0•Updated Apr 30, 2024Apr 30, 2024

• GeneosCollaboration

  Public
  Repository for R code for single cell sequencing analysis published in Yarchoan, M., Gane, E.J., Marron, T.U. et al. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med (2024).

  R

  •1•7•0•0•Updated Apr 8, 2024Apr 8, 2024

• git-test

  Public
  0•0•1•1•Updated Mar 15, 2024Mar 15, 2024

• J15221_trial_paper

  Public
  HTML

  •0•0•0•0•Updated Jan 30, 2024Jan 30, 2024

• pycogaps

  Public
  python API to the CoGAPS NMF package

  Python

  •

  GNU General Public License v2.0

  •6•18•21•3•Updated Dec 20, 2023Dec 20, 2023

• PacVAX2_pancvaxICI_scRNAseq

  Public
  scRNAseq and survival analysis in Panc02-bearing mice treated with PancVAX and immune checkpoint inhibition

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 12, 2023Oct 12, 2023

• J1568_Bulk

  Public
  Repository created to house code pertaining to the J1568 MultiOmics Paper

  Shell

  •2•0•0•0•Updated Aug 15, 2023Aug 15, 2023

• SpaceMarkersGuide

  Public
  HTML

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

• PDAC_Atlas

  Public
  Analysis workflow for all data present in our PDAC Atlas Manuscript titled, "Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma"

  R

  •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

• CoGAPSGuide

  Public
  0•0•0•0•Updated May 24, 2023May 24, 2023

• RNAForecasterPaperCode

  Public
  Julia

  •2•4•0•0•Updated May 16, 2023May 16, 2023

• splicemutr_paper

  Public
  Generating the figures from supplementary data for the splicemutr paper

  HTML

  •0•0•0•0•Updated May 8, 2023May 8, 2023

• pycogaps-gpn

  Public
  PyCoGAPS for support with GenePattern Notebook.

  Python

  •1•0•0•1•Updated Mar 5, 2023Mar 5, 2023

• pycogaps-docker

  Public
  PyCoGAPS with Docker support

  C++

  •0•0•0•0•Updated Mar 5, 2023Mar 5, 2023