CARNIVAL - A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

Last updated 5 months ago

transcriptomicsgeneexpressionnetworkcausal-modelsfootprintsinteger-linear-programmingpathway-enrichment-analysis

9.03 score 57 stars 1 dependents 90 scripts 418 downloads

cosmosR - COSMOS (Causal Oriented Search of Multi-Omic Space)

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.

Last updated 5 months ago

cellbiologypathwaysnetworkproteomicsmetabolomicstranscriptomicsgenesignalingdata-integrationmetabolomic-datanetwork-modellingphosphoproteomics

7.22 score 59 stars 35 scripts 244 downloads

CellNOptR - Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

Last updated 10 days ago

cellbasedassayscellbiologyproteomicspathwaysnetworktimecourseimmunooncology

6.95 score 6 dependents 98 scripts 436 downloads

CNORode - ODE add-on to CellNOptR

Logic based ordinary differential equation (ODE) add-on to CellNOptR.

Last updated 5 months ago

immunooncologycellbasedassayscellbiologyproteomicsbioinformaticstimecourse

5.74 score 1 dependents 37 scripts 316 downloads

CNORfeeder - Integration of CellNOptR to add missing links

This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.

Last updated 14 days ago

cellbasedassayscellbiologyproteomicsnetworkinference

3.78 score 9 scripts 302 downloads