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    37 repositories

    • bcm3

      Public
      BCM3 - Bayesian Inference for Computational Models
      C++
      •
      Apache License 2.0
      •1•0•0•0•Updated Sep 2, 2026Sep 2, 2026

    • sobolev_alignment

      Public
      Sobolev alignment of deep probabilistic models for comparing single cell profiles
      pythondeep-learningclinical
      pythondeep-learningclinicalgene-expressioncancer-genomicsscrna-seqsingle-cellvariational-autoencodercell-linesscanpy
      Python
      •
      MIT License
      •2•6•0•2•Updated Aug 31, 2026Aug 31, 2026

    • NKI_pancancer_neoadj_io

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 31, 2026Aug 31, 2026

    • Marlin

      Public
      MARker-informed Label INference (Marlin)
      R
      •0•0•0•0•Updated Aug 12, 2026Aug 12, 2026

    • ICRA-trial-code-and-data

      Public
      1•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • cell2sentence

      Public
      Cell2Sentence: Teaching Large Language Models the Language of Biology
      Jupyter Notebook
      •
      Other
      •132•1•0•0•Updated Feb 7, 2026Feb 7, 2026

    • mvdens

      Public
      Multivariate probability density approximation R package
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Nov 19, 2025Nov 19, 2025

    • DISCOVER

      Public
      DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
      pythonbioinformaticsr
      pythonbioinformaticsrgenomics
      Fortran
      •
      Apache License 2.0
      •8•34•8•0•Updated May 1, 2025May 1, 2025

    • chemo_and_bladder_TME

      Public
      HTML
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 10, 2024May 10, 2024

    • PRECISE

      Public
      Python
      •
      MIT License
      •4•8•0•1•Updated Feb 1, 2024Feb 1, 2024

    • scMeMo-paper

      Public
      R
      •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • TRANSACT_manuscript

      Public
      Scripts supporting TRANSACT manuscript
      Python
      •
      MIT License
      •6•8•1•1•Updated Aug 17, 2023Aug 17, 2023

    • ppbc

      Public
      Post-partum breast cancer
      R
      •
      MIT License
      •1•1•0•0•Updated Jul 4, 2023Jul 4, 2023

    • sobolev_alignment_manuscript

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 15, 2023Mar 15, 2023

    • TRANSACT

      Public
      Python implementation of TRANSACT, a tool to transfer non-linear predictors of drug response from model systems to tumors.
      pythonkernel-methodsinterpretability
      pythonkernel-methodsinterpretabilitycell-linestumorsdrug-response-predictiondrug-responseprincipal-vectors
      HTML
      •
      MIT License
      •3•6•0•0•Updated Nov 21, 2022Nov 21, 2022

    • Percolate

      Public
      Implementation of Percolate, an exponential family JIVE statistical model for multi-view integration
      machine-learningpytorchexponential-family
      machine-learningpytorchexponential-familymulti-omicsjivemulti-viewdrug-response-predictionglm-pca
      Python
      •
      MIT License
      •0•1•1•0•Updated Oct 23, 2022Oct 23, 2022

    • Percolate_manuscript

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 23, 2022Oct 23, 2022

    • precision-immune-analyses

      Public
      Analyses for the PRECISION DCIS immune paper (in press)
      R
      •0•1•0•0•Updated Jun 30, 2022Jun 30, 2022

    • prepost_neoadjuvant

      Public
      Apache License 2.0
      •1•0•0•0•Updated Apr 4, 2022Apr 4, 2022

    • Tumor-educated-platelets

      Public
      Code accompanying the publication "Tumor educated platelets for breast cancer detection"
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 10, 2022Mar 10, 2022

    • funcsfa

      Public
      Functional Sparse-Factor Analysis
      Python
      •
      Apache License 2.0
      •0•1•1•0•Updated Feb 14, 2022Feb 14, 2022

    • RUBIC

      Public
      RUBIC detects recurrent copy number aberrations.
      R
      •
      Apache License 2.0
      •8•4•0•0•Updated Aug 30, 2021Aug 30, 2021

    • flexgsea-r

      Public
      Flexible gene set enrichment analysis
      bioinformaticsrgene-expression
      bioinformaticsrgene-expressiongene-set-enrichmentpathway-analysisgsea
      R
      •
      Apache License 2.0
      •2•10•3•0•Updated Aug 30, 2021Aug 30, 2021

    • imagene-analysis

      Public
      Radiogenomic analysis of breast cancer by linking MRI phenotypes with tumor gene expression
      Python
      •
      MIT License
      •1•4•0•0•Updated Jun 9, 2021Jun 9, 2021

    • won-parafac

      Public
      Weighted orthogonal non-negative (WON) parallel factor analsyis (PARAFAC)
      bioinformaticsgenomicsmatlab
      bioinformaticsgenomicsmatlabunsupervised-learningparafac
      MATLAB
      •
      Apache License 2.0
      •2•2•1•0•Updated May 17, 2021May 17, 2021

    • TANDEM

      Public
      A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response predic…
      R
      •0•4•0•0•Updated Nov 25, 2019Nov 25, 2019

    • PRECISE_figures

      Public
      Jupyter notebooks and code to reproduce figures
      Jupyter Notebook
      •
      Apache License 2.0
      •3•0•0•0•Updated Oct 2, 2019Oct 2, 2019

    • cnr

      Public
      A method for network reconstruction and quantification from perturbation experiments
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 11, 2019Sep 11, 2019

    • CNR-analyses

      Public
      Notebooks to reproduce the figures from CNR manuscript (Bosdriesz et al., Bioinformatics, 2018)
      Jupyter Notebook
      •0•0•0•0•Updated Nov 7, 2018Nov 7, 2018

    • iTOP

      Public
      Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples.
      R
      •0•1•0•0•Updated Jun 13, 2018Jun 13, 2018
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