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    34 repositories

    • sobolev_alignment

      Public
      Sobolev alignment of deep probabilistic models for comparing single cell profiles
      pythondeep-learningclinicalgene-expressioncancer-genomicsscrna-seqsingle-cellvariational-autoencodercell-linesscanpy
      Python
      •
      MIT License
      •2•6•0•2•Updated Dec 22, 2025Dec 22, 2025

    • cell2sentence

      Public
      Cell2Sentence: Teaching Large Language Models the Language of Biology
      Jupyter Notebook
      •
      Other
      •110•1•0•0•Updated Dec 5, 2025Dec 5, 2025

    • mvdens

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

    • bcm3

      Public
      BCM3 - Bayesian Inference for Computational Models
      C++
      •
      Apache License 2.0
      •1•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • DISCOVER

      Public
      DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
      pythonbioinformaticsrgenomics
      Fortran
      •
      Apache License 2.0
      •8•32•8•0•Updated May 1, 2025May 1, 2025

    • chemo_and_bladder_TME

      Public
      HTML
      •
      GNU General Public License v3.0
      •0•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•6•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-methodsinterpretabilitycell-linestumorsdrug-response-predictiondrug-responseprincipal-vectors
      HTML
      •
      MIT License
      •3•3•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-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-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)
      bioinformaticsgenomicsmatlabunsupervised-learningparafac
      MATLAB
      •
      Apache License 2.0
      •2•1•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 prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream featu…
      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

    • MixedIC50

      Public
      A non-linear mixed effects model for estimating compound sensitivity
      HTML
      •1•4•0•0•Updated Apr 10, 2018Apr 10, 2018

    • iTOP-RMarkdown

      Public
      An R Markdown file containing code to reproduce all figures from our iTOP publication
      0•0•0•0•Updated Apr 4, 2018Apr 4, 2018

    • multitask_vi

      Public
      The Multitask Variable Importance (Multitask VI) is a modified version of the permuted variable importance score for Random Forests. Essentially, for a Random Forest trained simultaneously for multiple response vectors, it allows the inference of variable importance scores per variable and per task.
      Python
      •0•2•0•0•Updated Jan 9, 2018Jan 9, 2018