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cnor_cholreg

cnorfeeder

CellNOptR add-on that permits to extend a network with links derived from literature

cnorfuzzy

CellNOptR extension using constrained fuzzy logic

cnorode

add-on for CellNOptR using logic based differential equations

cnorode2017

modified version of CNORode including: steady state penalty, L1 regularisation, bootstrap, new transfer function

cnorprob

Probabilistic logic version of CellNOpt (derived from FALCON)

cnov2

Main repository for the new CellNOpt features (CNOv2)

codax

Neural Logic ODEs for Cell Signaling Inference with JAX

collectri

Gene regulatory network containing signed transcription factor-target gene interactions

combi-seq-analysis

Analysis code for Combi-Seq paper

combims

combiMS code for Prediction of combination therapy based on perturbation modeling of the multiple sclerosis signaling network. Code started by Marti at EBI on Feb 2013

conformationomic_yeast_picotti_2020

Conformationomic dataset (+phospho) of yeast osmotic stress to explore possibilities with this type of data.

conservedfootprints

Transfer of regulatory knowledge from human to mouse for functional genomics analysis

corneto

CORNETO: A Unified Omics-Driven Framework for Network Inference

cosmos_meta_pkn_redhuman

new lighter and streamlined PKN generation, based on redHuman reaction network

cosmos_msb

code for the COSMOS study in MSB

cosmos_prototype

cosmosr

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

covid19

We use our tools to analysis Covid19 RNAseq datasets

covid19_drugsignatures

covid19_phospho

Analysis of Phosphoproteomics/Transcriptomics datasets related to SARS-CoV-2 infection

covid_bulk_liver

Functional analysis of Liver samples from COVID patients

covid_intestinalorganoids

Saezlab tools on Intestinal organoids treated with Sars-CoV-2 for 60 hours

cpt_qsptutorial

Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology

crc-pathway-biomarkers

Cell-type specific parameters of signalling pathway models as biomarkers for drug sensitivity

crcdiet

CRCDiet

cxcl4_gleitz_paper_2019

cyrface

Bridging Cytoscape with R

cysbgn

cytocopter

CellNOptR in Cytoscape