CCB, NKI (@NKI-CCB)
Guthub

NKI-CCB

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Top repositories

1

DISCOVER

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
Fortran
27
star
2

flexgsea-r

Flexible gene set enrichment analysis
R
9
star
3

PRECISE

Python
7
star
4

TRANSACT_manuscript

Scripts supporting TRANSACT manuscript
Python
5
star
5

sobolev_alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles
Python
5
star
6

imfusion

Tool for identifying transposon insertions and their effects from RNA-seq data.
Python
5
star
7

MixedIC50

A non-linear mixed effects model for estimating compound sensitivity
HTML
4
star
8

imagene-analysis

Radiogenomic analysis of breast cancer by linking MRI phenotypes with tumor gene expression
Python
4
star
9

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 features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.
R
4
star
10

RUBIC

RUBIC detects recurrent copy number aberrations.
R
3
star
11

TRANSACT

Python implementation of TRANSACT, a tool to transfer non-linear predictors of drug response from model systems to tumors.
HTML
2
star
12

dids

R package for the Detection of Imbalanced Differential Signal (DIDS) algorithm.
R
2
star
13

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
2
star
14

iTOP

Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples.
R
1
star
15

ppbc

Post-partum breast cancer
R
1
star
16

funcsfa

Functional Sparse-Factor Analysis
Python
1
star
17

cimpl

Common Insertion Site Mapping Platform implemented as an R package for statistical analysis of retroviral insertional mutagenesis screens.
HTML
1
star
18

won-parafac

Weighted orthogonal non-negative (WON) parallel factor analsyis (PARAFAC)
MATLAB
1
star
19

Percolate

Implementation of Percolate, an exponential family JIVE statistical model for multi-view integration
Python
1
star