Repositories list

• SCWorkflow

  Public
  Workflow Package for Analysis of Single Cell Data

  R

  •

  MIT License

  •2•0•4•3•Updated Mar 4, 2026Mar 4, 2026

• MOSuite-CodeOcean

  Public
  Code Ocean pipeline for MOSuite

  bulk-rna-seqcode-oceanmosuite

  bulk-rna-seqcode-oceanmosuite

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

• MOSuite-Nextflow

  Public
  Nextflow pipeline for Multi-OmicsSuite

  pipelinenextflow

  pipelinenextflow

  Nextflow

  •

  MIT License

  •1•0•0•0•Updated Feb 6, 2026Feb 6, 2026

• giotto-st-pipeline

  Public

  NIDAP-Community/giotto-st-pipeline’s past year of commit activity
  This is a singularity package that will run the Giotto pipeline for Spatial Transcriptomics

  R

  •0•0•0•0•Updated Jan 13, 2026Jan 13, 2026

• multi-gene-correlations

  Public
  Containerized R workflow that correlates gene panels against signature scores, producing publication-ready tables and plots with Docker and Singularity support.

  R

  •1•0•0•0•Updated Jan 13, 2026Jan 13, 2026

• ghcr-hello-world

  Public
  Test for Galaxy

  Dockerfile

  •

  MIT License

  •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

• l2p-galaxy-tool

  Public
  L2P pathway enrichment analysis tool for Galaxy with automated Docker builds

  R

  •

  MIT License

  •1•0•0•0•Updated Dec 17, 2025Dec 17, 2025

• CPTR-10-Tosato-Mouse-WTA-DSP-Analysis

  Public
  R

  •1•0•0•0•Updated Sep 9, 2025Sep 9, 2025

• nidapFunctions

  Public
  This package will contain all NIDAP specific functions

  R

  •

  Other

  •1•0•0•0•Updated Aug 22, 2025Aug 22, 2025

• DSP_Analysis

  Public
  A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling

  R

  •1•0•0•0•Updated Jul 26, 2025Jul 26, 2025

• Epigenetic-plus-Cytokine-Therapy-Evades-CPB-Resistance-by-Potentiating-CTL-Stem-Immunity-Clusters

  Public
  This code repo accompanies the paper entitled "Epigenetic plus Cytokine Therapy Evades Checkpoint Blockade Resistance by Potentiating Cytotoxic CD8+ T Cells wit…

  R

  •

  MIT License

  •0•0•0•0•Updated Jan 18, 2025Jan 18, 2025

• 3D-intercellular-assembly-of-decellularized-matrix-recapitulates-in-vivo-tumor-heterogeneity

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• CPTR-11-Beck-Canine-OsteoSarcoma-DSP-Analysis

  Public
  R

  •1•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• CPTR-12-Wang-DSP-Analysis

  Public
  R

  •1•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• ShinyQC-Inspector

  Public
  This application will allow for inspection of PCA outlier data, associating it with quality metrics

  R

  •

  MIT License

  •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• Effects-of-a-humanized-CD47-antibody-and-recombinant-SIRPalpha-proteins-on-TNBC-stem-cells

  Public
  R

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• CPTR_5_DSP_Krug

  Public
  HTML

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

• CPTR-9-Weigert-DSP-Analysis

  Public
  HTML

  •1•0•0•0•Updated Jul 24, 2024Jul 24, 2024

• TRAIL-Induced-NFKB2-Pathway-Promotes-Neutrophil-Chemotaxis-and-Immune-Suppression-in-TNBC

  Public
  This code repo accompanies the paper entitled "TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in trip…

  MIT License

  •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

• Regulation-of-Extramedullary-Erythropoiesis-by-CD47-and-THBS1

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Jul 9, 2024Jul 9, 2024

• HIV-vaccine-candidate-efficacy

  Public
  This code accompanies the paper entitled: HIV vaccine candidate efficacy mediated by cyclic AMP-dependent efferocytosis and V2-specific ADCC

  R

  •

  MIT License

  •0•0•0•0•Updated Jun 19, 2024Jun 19, 2024

• Adoptive_transfer_of_membrane-restricted_IL-12-TCR_Tcells

  Public
  0•0•0•0•Updated Jun 5, 2024Jun 5, 2024

• Protection-against-intrarectal-SIV-by-a-SHIV-vaccine

  Public
  Code relating to some of the results from "Innate protection against intrarectal SIV acquisition by a live SHIV vaccine". Code will be available upon publicatio…

  MIT License

  •0•0•0•0•Updated May 28, 2024May 28, 2024

• CPTR_6_DSP_Annunziata

  Public
  1•0•0•0•Updated Mar 21, 2024Mar 21, 2024

• DSPWorkflow

  Public
  HTML

  •

  MIT License

  •3•5•19•0•Updated Feb 21, 2024Feb 21, 2024

• Knockout-of-CD47-and-IFT57-in-thyroid-cancer

  Public
  0•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• A-Knock-In-Mouse-Model-of-Thymoma-With-the-GTF2I-L424H-Mutation

  Public
  MIT License

  •0•0•0•0•Updated Dec 29, 2023Dec 29, 2023

• Characterization-of-Immunogenicity-of-Malignant-Cells

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Dec 29, 2023Dec 29, 2023

• Murine-Allogeneic-CAR-T-Cells

  Public
  R

  •0•0•0•0•Updated Dec 28, 2023Dec 28, 2023

• Anti-cancer-activity-of-verteporfin-in-cholangiocarcinoma

  Public
  This repo contains the code accompanying the paper titled: Anti-cancer activity of verteporfin in cholangiocarcinoma

  R

  •0•0•0•0•Updated Dec 28, 2023Dec 28, 2023