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acsnminer

R package for enrichment/depletion analysis of ACSN maps and gmt files

amonet

Artificial Molecular Network: graph learning for cancer survival prediction from targeted sequencing

binom

binom-3.0

BiNoM (Biological Network Manager) is a Cytoscape 3 app currently under developement by the Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

biodica

"Independent Component Analysis of BIg Omics Data"

biodica-environment

bionetworks_tutorial_icsb2016

cbiofetchr

R package to fetch data from cBioPortal using a list of genes.

cd2sbgnml

Translation between CellDesigner-flavoured SBML and SBGN-ML

celldesigner_networks_map_integration_procedure

Procedure for integration of networks of CellDesigner maps

cfnetwork

Codes to reproduce the analyses and the construction of the CF signalling network.

cfnetwork_cytoscape

Repository for the cytoscape session of the CF network paper

clintrajan

Finding trajectories, bifurcations and quantifying pseudotime in large clinical datasets

clustmmra

clustmmra_v2

A scalable version of the clustMMRA pipeline for the identification of genomically co-clustered microRNAs driving cancer subtypes.

colosys_model

covid19

Rapid prototyping coalition for SARS-CoV-2 tissue infection dynamics. (integrated model)

curie-permedcoe-summer-school-2023

deconica

Deconvolution of transcriptome through Immune Component Analysis

dedal

DeDaL (Data-Driven network Layout) is a Cytoscape 3.0 app developed by the Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

dockercollection

A collection of Docker images to run different softwares

eccb2020-t05

Material for the tutorial 05 of ECCB (Computational modelling of cellular processes: regulatory vs metabolic systems)

elmap

Elastic map

elpigraph.m

Matlab implementation of the Elastic Principal Graphs (ElPiGraph) method

elpigraph.p

Python implementation of the Elastic Principal Graph algorithm with multi-cpu and gpu support

elpigraph.r

An R package to construct Elastic Principal Graphs

ewingsarcoma_omics_atlas

ewingsinglecelldataanalysis

Code accompanying the manuscript "Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution"

exact-stoch-log-mod

ExaStoLog: a MATLAB toolbox for EXAct calculation of STOchastic LOGical models