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@NKI-CCB

CCB, NKI

Computation Cancer Biology Group, the Netherlands Cancer Institute

Pinned repositories

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

    Fortran 14 6

  2. Flexible gene set enrichment analysis

    R 7 2

  3. A method for network reconstruction and quantification from perturbation experiments

    Python

  4. 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 …

    R 2 1

  5. Weighted orthogonal non-negative (WON) parallel factor analsyis (PARAFAC)

    MATLAB 1 2

Repositories

  • R Apache-2.0 2 7 3 0 Updated Nov 18, 2020
  • Python MIT 1 4 0 0 Updated Nov 11, 2020
  • TRANSACT_manuscript

    Scripts supporting TRANSACT manuscript

    Jupyter Notebook MIT 1 2 0 1 Updated Nov 4, 2020
  • TRANSACT

    Python implementation of TRANSACT, a tool to transfer non-linear predictors of drug response from model systems to tumors.

    Python MIT 0 0 0 0 Updated Oct 2, 2020
  • imagene-analysis

    Radiogenomic analysis of breast cancer by linking MRI phenotypes with tumor gene expression

    0 0 0 0 Updated Apr 30, 2020
  • won-parafac

    Weighted orthogonal non-negative (WON) parallel factor analsyis (PARAFAC)

    MATLAB Apache-2.0 2 1 0 0 Updated Dec 4, 2019
  • mvdens

    Multivariate probability density approximation R package

    R Apache-2.0 0 0 1 0 Updated Nov 27, 2019
  • TANDEM

    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 1 2 0 0 Updated Nov 25, 2019
  • PRECISE_figures

    Jupyter notebooks and code to reproduce figures

    Jupyter Notebook Apache-2.0 1 0 0 0 Updated Oct 2, 2019
  • cnr

    A method for network reconstruction and quantification from perturbation experiments

    Python MIT 0 0 0 0 Updated Sep 11, 2019
  • DISCOVER

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

    Fortran Apache-2.0 6 14 1 0 Updated Jun 18, 2019
  • funcsfa

    Functional Sparse-Factor Analysis

    Python Apache-2.0 0 1 1 0 Updated Nov 21, 2018
  • CNR-analyses

    Notebooks to reproduce the figures from CNR manuscript (Bosdriesz et al., Bioinformatics, 2018)

    Jupyter Notebook 0 0 0 0 Updated Nov 7, 2018
  • iTOP

    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, 2018
  • MixedIC50

    A non-linear mixed effects model for estimating compound sensitivity

    HTML 1 3 0 0 Updated Apr 10, 2018
  • iTOP-RMarkdown

    An R Markdown file containing code to reproduce all figures from our iTOP publication

    0 0 0 0 Updated Apr 4, 2018
  • multitask_vi

    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, 2018
  • imfusion

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

    Python MIT 1 3 5 0 Updated Oct 17, 2017
  • RUBIC

    RUBIC detects recurrent copy number aberrations.

    R Apache-2.0 5 2 0 0 Updated Apr 24, 2017
  • cimpl

    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, 2017
  • dids

    R package for the Detection of Imbalanced Differential Signal (DIDS) algorithm.

    R 0 2 0 0 Updated Feb 3, 2017
  • kcrbm

    R code for Kernel Convolved Rule Based Mapping

    R 0 0 0 0 Updated Feb 1, 2017

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