Repositories list

• ispy2-r2r

  Public
  Running READII-2-ROQC on ISPY2

  HTML

  •0•0•0•1•Updated May 29, 2025May 29, 2025

• med-imagetools

  Public
  Transparent and reproducible medical image processing pipelines in Python.

  pythonmachine-learningdeep-learning+ 6dicomtorchpytorchmedicalnrrdnifti

  Python

  •

  MIT License

  •9•47•20•5•Updated May 29, 2025May 29, 2025

• readii_2_roqc

  Public
  Python

  •0•0•4•1•Updated May 29, 2025May 29, 2025

• ml-pipeline-aircheck

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated May 28, 2025May 28, 2025

• med-image_test-data

  Public
  Python

  •

  Other

  •0•2•0•0•Updated May 28, 2025May 28, 2025

• handbook

  Public
  Lab Handbook For BHKLab

  0•4•43•11•Updated May 26, 2025May 26, 2025

• readii

  Public
  Radiomic Extraction and Analysis for DICOM Images (READII)

  Jupyter Notebook

  •

  MIT License

  •0•5•27•2•Updated May 26, 2025May 26, 2025

• damply

  Public
  Data Management Plan made simple

  Python

  •0•0•1•0•Updated May 26, 2025May 26, 2025

• agony

  Public
  Agony implementation

  C++

  •0•1•0•1•Updated May 22, 2025May 22, 2025

• PharmacoGx

  Public
  R package to analyze large-scale pharmacogenomic datasets.

  datasetspharmacogxpharmacogenomic

  R

  •

  GNU General Public License v3.0

  •26•68•73•0•Updated May 22, 2025May 22, 2025

• staged-recipes

  Public
  A place to submit conda recipes before they become fully fledged conda-forge feedstocks

  Python

  •

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

  •5.3k•0•0•0•Updated May 22, 2025May 22, 2025

• ispy-readii

  Public
  Running READII on the I-SPY cohort for radiogenomic analysis.

  HTML

  •

  MIT License

  •1•0•0•0•Updated May 21, 2025May 21, 2025

• public_image_data_curation

  Public
  Code to collect info about publicly available medical image datasets for curation

  Jupyter Notebook

  •0•0•0•0•Updated May 21, 2025May 21, 2025

• bhklab-project-template

  Public
  Setup FAIR and DMP compliant projects with one command

  templatepixifair

  Python

  •

  MIT License

  •0•1•3•2•Updated May 20, 2025May 20, 2025

• project-template-test

  Public
  An example of exactly what the project template does!

  Jupyter Notebook

  •0•0•0•2•Updated May 20, 2025May 20, 2025

• genefu

  Public
  R package providing various functions relevant for gene expression analysis with emphasis on breast cancer.

  HTML

  •13•25•6•1•Updated May 20, 2025May 20, 2025

• orcestra-downloader

  Public
  Seamless CLI access to orcestra datasets

  Python

  •

  MIT License

  •1•0•3•1•Updated May 13, 2025May 13, 2025

• bhklab-website

  Public
  BHK Lab website

  JavaScript

  •0•0•4•0•Updated May 8, 2025May 8, 2025

• PredictioR

  Public
  An R Package for Biomarker Discovery in Immuno-Oncology Therapy Response

  HTML

  •

  MIT License

  •0•0•0•0•Updated May 5, 2025May 5, 2025

• ORCESTRA

  Public
  ORCESTRA is a new web application that enables users to search, request and manage pharmacogenomic datasets (PSets).

  JavaScript

  •

  Apache License 2.0

  •2•5•16•8•Updated May 2, 2025May 2, 2025

• Lung-Lesion-Treatment-Response-Prediction

  Public
  Code + Data for Lung Lesion Treatment Response Prediction

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

• MIRV

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

• PMATCH-web

  Public
  JavaScript

  •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

• SignatureSets

  Public
  Compendium of published molecular signatures

  HTML

  •

  MIT License

  •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

• pdxe-to-csv

  Public
  Python

  •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

• med-imagenet

  Public
  Med-ImageNet processing scripts via Med-ImageTools AutoPipeline

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Mar 27, 2025Mar 27, 2025

• AnnotationGx

  Public
  An R package to query various bio/chem-informatics databases APIs to construct annotation files.

  R

  •

  MIT License

  •1•1•7•0•Updated Mar 27, 2025Mar 27, 2025

• Xeva

  Public
  XEnograft Visualization & Analysis

  R

  •5•11•5•0•Updated Mar 20, 2025Mar 20, 2025

• PredictIO_Nextflow

  Public
  Nextflow

  •0•0•0•0•Updated Mar 16, 2025Mar 16, 2025

• snakemake-storage-plugin-orcestra

  Public
  Python

  •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025