Repositories list

• amtec_manuscript

  Public
  Workflow code supporting the manuscript 'Utilizing cohort-level and individual networks to predict best response in patients with metastatic triple negative breast cancer'

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

• TKG-DTI

  Public
  Prediction of drug-target interactions using a knowledge graph that includes the cancer targetome resource

  Jupyter Notebook

  •0•1•0•0•Updated Mar 11, 2025Mar 11, 2025

• AMLVAE

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

• hnscc_manuscript

  Public
  Workflow code supporting the manuscript 'Assessing Individual Head and Neck Squamous Cell Carcinoma Patient Response to Therapy Through Integration of Functional and Genomic Data'

  R

  •

  MIT License

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• hnscc_data

  Public
  Processed data to accompany 'Assessing Individual Head and Neck Squamous Cell Carcinoma Patient Response to Therapy Through Integration of Functional and Genomic Data'

  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

• nvflare-cancer

  Public
  Using nvflare federated learning in a cancer research project

  Shell

  •

  Apache License 2.0

  •1•2•0•0•Updated Nov 27, 2024Nov 27, 2024

• MMDL_FL

  Public
  Updating and refactoring to support a federated learning scenario

  2•1•0•0•Updated Jul 12, 2024Jul 12, 2024

• beataml2.0_data

  Public
  Data accompanying the BeatAML2.0 manuscript

  Creative Commons Attribution 4.0 International

  •2•5•0•0•Updated Feb 13, 2024Feb 13, 2024

• SIG

  Public
  Workflows and code for the Systems Immunogenetics project

  Jupyter Notebook

  •3•1•0•0•Updated Nov 10, 2023Nov 10, 2023

• bias_fairness_in_ml

  Public
  Applied Labs for 'Achieving Fairness in ML/AI'

  HTML

  •0•0•0•0•Updated Jul 18, 2023Jul 18, 2023

• beataml2_manuscript

  Public
  Workflow to reproduce results and figures for the second BeatAML manuscript

  R

  •3•10•0•0•Updated Jun 28, 2022Jun 28, 2022

• cycIF-workflow

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jun 11, 2020Jun 11, 2020

• HNSCC_Notebook

  Public
  Workflow of light/dark pathways in HNSCC

  HTML

  •1•0•0•0•Updated Oct 24, 2019Oct 24, 2019

• packageDir

  Public
  pathway analysis package for HNSCC paper

  R

  •0•1•0•0•Updated Sep 9, 2019Sep 9, 2019

• immpload

  Public
  Immport upload preparation

  immport

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Sep 4, 2019Sep 4, 2019

• beataml_genomics

  Public
  Public version of BeatAML workflow

  Scala

  •0•0•0•0•Updated Jul 2, 2019Jul 2, 2019

• openCyto

  Public
  A package that provides data analysis pipeline for flow cytometry.

  R

  •30•0•0•0•Updated Nov 8, 2017Nov 8, 2017

• batchtools

  Public
  Tools for computation on batch systems

  R

  •

  GNU Lesser General Public License v3.0

  •51•0•0•0•Updated May 5, 2017May 5, 2017

• BatchJobs

  Public
  BatchJobs: Batch computing with R

  R

  •

  Other

  •20•0•0•0•Updated Oct 10, 2016Oct 10, 2016

• HitWalker2

  Public
  HTML

  •3•5•0•0•Updated Jan 4, 2016Jan 4, 2016

• vcf2maf

  Public
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

  Perl

  •

  Apache License 2.0

  •219•0•0•0•Updated Jul 13, 2015Jul 13, 2015

• gatk-protected

  Public
  GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

  Java

  •126•0•0•0•Updated May 18, 2015May 18, 2015

• HTCondor_drivers

  Public
  Scala

  •0•0•0•0•Updated May 15, 2015May 15, 2015

• pathLayerDistributionVersion2

  Public
  Experimental version, ie: not guaranteed to function correctly!

  R

  •1•0•0•0•Updated Feb 17, 2015Feb 17, 2015