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 downloadsCellNOptR - 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 9 days ago
cellbasedassayscellbiologyproteomicspathwaysnetworktimecourseimmunooncology
6.95 score 6 dependents 98 scripts 436 downloadsCNORode - 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 downloadsCNORfeeder - 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 13 days ago
cellbasedassayscellbiologyproteomicsnetworkinference
3.78 score 9 scripts 302 downloads