Repositories list

• sobolev_alignment

  Public
  Sobolev alignment of deep probabilistic models for comparing single cell profiles

  deep-learningclinicalgene-expression+ 11cancer-genomicsscrna-seqsingle-cellvariational-autoencodercell-linesscanpypre-clinical+ 4

  Python

  •

  MIT License

  •2•5•0•1•Updated Nov 11, 2024Nov 11, 2024

• bcm3

  Public
  BCM3 - Bayesian Inference for Computational Models

  C++

  •

  Apache License 2.0

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

• PRECISE

  Public
  Python

  •

  MIT License

  •2•7•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

  •3•5•1•1•Updated Aug 17, 2023Aug 17, 2023

• ppbc

  Public
  Post-partum breast cancer

  R

  •

  MIT License

  •0•1•0•0•Updated Jul 4, 2023Jul 4, 2023

• DISCOVER

  Public
  DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

  pythonbioinformaticsr+ 1genomics

  Fortran

  •

  Apache License 2.0

  •7•28•7•0•Updated May 12, 2023May 12, 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+ 5cell-linestumorsdrug-response-predictiondrug-responseprincipal-vectors

  HTML

  •

  MIT License

  •2•2•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+ 5multi-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•0•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

  •0•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

  •7•3•0•0•Updated Aug 30, 2021Aug 30, 2021

• flexgsea-r

  Public
  Flexible gene set enrichment analysis

  bioinformaticsrgene-expression+ 3gene-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+ 2unsupervised-learningparafac

  MATLAB

  •

  Apache License 2.0

  •2•1•1•0•Updated May 17, 2021May 17, 2021

• mvdens

  Public
  Multivariate probability density approximation R package

  R

  •

  Apache License 2.0

  •1•0•1•0•Updated Nov 27, 2019Nov 27, 2019

• 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

  •2•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

• imfusion

  Public
  Tool for identifying transposon insertions and their effects from RNA-seq data.

  Python

  •

  MIT License

  •1•5•7•0•Updated Oct 17, 2017Oct 17, 2017

• cimpl

  Public
  Common Insertion Site Mapping Platform implemented as an R package for statistical analysis of retroviral insertional mutagenesis screens.

  HTML

  •1•1•1•0•Updated Mar 22, 2017Mar 22, 2017