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cxcl4_gleitz_paper_2019

cyrface

Bridging Cytoscape with R

cysbgn

cytocopter

CellNOptR in Cytoscape

darkgenes_annotations

Pipeline for TF & pathway enrichments of unannotated genes (TransQST in collaboration with IMIM and Maastricht University)

data_tools

Collection of Python functions and classes designed to make data scientists' life easier.

decoupler

R package to infer biological activities from omics data using a collection of methods.

decoupler-py

Python package to perform enrichment analysis from omics data.

decoupler_manuscript

Code to reproduce the results from decoupleR's manuscript

decouplerbench

Package to benchmark methods from decoupleR

dorothea

R package to access DoRothEA's regulons

dorothea-py

Dorothea package in Python

dot

DOT

dream2019_single_cell

preparation for the single cell DREAM challenge 2019

dream2019_single_cell_scoring

Scoring scripts and evaluation of teams

dream_hf_microbiome

Predict incident risk for heart failure in human population studies by combining fecal microbiome composition and host information

drugvsdisease

DvD: An R and Cytoscape plug-in for comparing Drug and Disease profiles

ebits

R modules for common tasks

eccb2022_sc_funcomics

Functional analysis of single-cell transcriptomics

edn_phospho

Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

egfrslopes

factor_cosmos

Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.

flake8-kwargs-spaces

Flake8 plugin to check for spaces around equals sign when passing keyword arguments

flop

FunctionaL Omics Processing platform

footprintmethods_on_scrnaseq

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

footprints

Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"

fosbe2019

Dynamic-Feeder implementation

funki

FUNctional analysis worKflows Interface

funkyshiny_cosmos_tuto

gdsc_footprints

decoupleR footprints on GDSC basal expression dataset