CCB, NKI
- Amsterdam, the Netherlands
- http://ccb.nki.nl
Pinned repositories
Repositories
-
flexgsea-r
Flexible gene set enrichment analysis
-
TRANSACT_manuscript
Scripts supporting TRANSACT manuscript
-
TRANSACT
Python implementation of TRANSACT, a tool to transfer non-linear predictors of drug response from model systems to tumors.
-
imagene-analysis
Radiogenomic analysis of breast cancer by linking MRI phenotypes with tumor gene expression
-
won-parafac
Weighted orthogonal non-negative (WON) parallel factor analsyis (PARAFAC)
-
mvdens
Multivariate probability density approximation R package
-
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…
-
PRECISE_figures
Jupyter notebooks and code to reproduce figures
-
cnr
A method for network reconstruction and quantification from perturbation experiments
-
DISCOVER
DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
-
funcsfa
Functional Sparse-Factor Analysis
-
CNR-analyses
Notebooks to reproduce the figures from CNR manuscript (Bosdriesz et al., Bioinformatics, 2018)
-
iTOP
Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples.
-
MixedIC50
A non-linear mixed effects model for estimating compound sensitivity
-
iTOP-RMarkdown
An R Markdown file containing code to reproduce all figures from our iTOP publication
-
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.
-
imfusion
Tool for identifying transposon insertions and their effects from RNA-seq data.
-
RUBIC
RUBIC detects recurrent copy number aberrations.
-
cimpl
Common Insertion Site Mapping Platform implemented as an R package for statistical analysis of retroviral insertional mutagenesis screens.
-
dids
R package for the Detection of Imbalanced Differential Signal (DIDS) algorithm.
-
kcrbm
R code for Kernel Convolved Rule Based Mapping