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    80 repositories

    • CoGAPS

      Public
      Bayesian MCMC matrix factorization algorithm
      machine-learningbioinformaticsbayesian-inferencesingle-cell-rna-seqnon-negative-matrix-factorizationhuman-cell-atlas
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •17•69•23•1•Updated Jul 9, 2025Jul 9, 2025

    • Differential_Cell_Signaling_Test

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • btc-spatial-pipelines

      Public
      Nextflow spatial pipelines (for Spatial Transcriptomics, IMC, etc.)
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • pycogaps

      Public
      python API to the CoGAPS NMF package
      Python
      •
      GNU General Public License v2.0
      •6•19•21•1•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 Palmer.
      C++
      •
      GNU Affero General Public License v3.0
      •1•0•1•1•Updated May 12, 2025May 12, 2025

    • dpt-combined-analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 8, 2025May 8, 2025

    • Human_PanIN_Spatial_Analysis

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 7, 2025May 7, 2025

    • J1798_trial_paper

      Public
      scripts for the J1798 trial paper
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2025Mar 19, 2025

    • J15221_trial_paper

      Public
      HTML
      •0•0•0•0•Updated Mar 19, 2025Mar 19, 2025

    • dpt-visium-notebook

      Public
      Nextflow
      •0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • onboarding

      Public
      Ruby
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • 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
      •8•5•5•4•Updated Feb 10, 2025Feb 10, 2025

    • bayestme

      Public
      BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data
      Jupyter Notebook
      •
      Other
      •4•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • fertiglab.github.io

      Public
      SCSS
      •1•0•1•0•Updated Jan 29, 2025Jan 29, 2025

    • spatial-pipeline

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

    • HCCTLS

      Public
      R
      •2•2•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

    • 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

    • splicemutr

      Public
      R
      •
      GNU General Public License v3.0
      •1•6•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
      •1•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
      •886•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•3•1•Updated Mar 15, 2024Mar 15, 2024

    • 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