CCB, NKI

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32 repositories

bcm3
Public
BCM3 - Bayesian Inference for Computational Models
C++
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Apache License 2.0
•1•0•0•0•Updated Dec 30, 2024Dec 30, 2024
sobolev_alignment
Public
Sobolev alignment of deep probabilistic models for comparing single cell profiles
deep-learning clinical gene-expression cancer-genomics scrna-seq single-cell variational-autoencoder cell-lines scanpy pre-clinical
Python
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MIT License
•2•5•0•1•Updated Dec 23, 2024Dec 23, 2024
PRECISE
Public
Python
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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
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MIT License
•3•5•1•1•Updated Aug 17, 2023Aug 17, 2023
ppbc
Public
Post-partum breast cancer
R
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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
python bioinformatics r genomics
Fortran
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Apache License 2.0
•7•28•7•0•Updated May 12, 2023May 12, 2023
sobolev_alignment_manuscript
Public
Jupyter Notebook
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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
•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-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
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GNU General Public License v3.0
•0•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
•7•3•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
mvdens
Public
Multivariate probability density approximation R package
R
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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
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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
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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•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
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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•2•0•Updated Mar 22, 2017Mar 22, 2017