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 27 days ago
transcriptomicsgeneexpressionnetworkcausal-modelsfootprintsinteger-linear-programmingpathway-enrichment-analysis
8.18 score 57 stars 1 packages 88 scripts 246 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 27 days ago
cellbiologypathwaysnetworkproteomicsmetabolomicstranscriptomicsgenesignalingdata-integrationmetabolomic-datanetwork-modellingphosphoproteomics
7.20 score 56 stars 35 scripts 188 downloadsCNORode - ODE add-on to CellNOptR
Logic based ordinary differential equation (ODE) add-on to CellNOptR.
Last updated 27 days ago
immunooncologycellbasedassayscellbiologyproteomicsbioinformaticstimecourse
6.22 score 1 packages 37 scripts 242 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 27 days ago
cellbasedassayscellbiologyproteomicspathwaysnetworktimecourseimmunooncology
5.72 score 6 packages 98 scripts 294 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 27 days ago
cellbasedassayscellbiologyproteomicsnetworkinference
3.60 score 9 scripts 242 downloads