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35 repositories

bcm3
Public
BCM3 - Bayesian Inference for Computational Models
C++
•
Apache License 2.0
•1•0•0•0•Updated Feb 20, 2026Feb 20, 2026
sobolev_alignment
Public
Sobolev alignment of deep probabilistic models for comparing single cell profiles
python deep-learning clinical gene-expression cancer-genomics scrna-seq single-cell variational-autoencoder cell-lines scanpy
Python
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MIT License
•2•6•0•2•Updated Feb 16, 2026Feb 16, 2026
NKI_pancancer_neoadj_io
Public
Python
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MIT License
•0•0•0•0•Updated Feb 12, 2026Feb 12, 2026
cell2sentence
Public
Cell2Sentence: Teaching Large Language Models the Language of Biology
Jupyter Notebook
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Other
•118•1•0•0•Updated Feb 7, 2026Feb 7, 2026
mvdens
Public
Multivariate probability density approximation R package
R
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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
python bioinformatics r genomics
Fortran
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Apache License 2.0
•8•32•8•0•Updated May 1, 2025May 1, 2025
chemo_and_bladder_TME
Public
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated May 10, 2024May 10, 2024
PRECISE
Public
Python
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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
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MIT License
•6•6•1•1•Updated Aug 17, 2023Aug 17, 2023
ppbc
Public
Post-partum breast cancer
R
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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.
python kernel-methods interpretability cell-lines tumors drug-response-prediction drug-response principal-vectors
HTML
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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-learning pytorch exponential-family multi-omics jive multi-view drug-response-prediction glm-pca
Python
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MIT License
•0•1•1•0•Updated Oct 23, 2022Oct 23, 2022
Percolate_manuscript
Public
Jupyter Notebook
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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
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Apache License 2.0
•0•1•1•0•Updated Feb 14, 2022Feb 14, 2022
RUBIC
Public
RUBIC detects recurrent copy number aberrations.
R
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Apache License 2.0
•8•4•0•0•Updated Aug 30, 2021Aug 30, 2021
flexgsea-r
Public
Flexible gene set enrichment analysis
bioinformatics r gene-expression gene-set-enrichment pathway-analysis gsea
R
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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
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MIT License
•1•4•0•0•Updated Jun 9, 2021Jun 9, 2021
won-parafac
Public
Weighted orthogonal non-negative (WON) parallel factor analsyis (PARAFAC)
bioinformatics genomics matlab unsupervised-learning parafac
MATLAB
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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 predic…
R
•0•4•0•0•Updated Nov 25, 2019Nov 25, 2019
PRECISE_figures
Public
Jupyter notebooks and code to reproduce figures
Jupyter Notebook
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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
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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•5•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