Showing 6 of total 6 results (show query)
bioc
CNORode:ODE add-on to CellNOptR
Logic based ordinary differential equation (ODE) add-on to CellNOptR.
Maintained by Attila Gabor. Last updated 5 months ago.
immunooncologycellbasedassayscellbiologyproteomicsbioinformaticstimecourse
5.74 score 37 scripts 1 dependentsbioc
bnem:Training of logical models from indirect measurements of perturbation experiments
bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).
Maintained by Martin Pirkl. Last updated 5 months ago.
pathwayssystemsbiologynetworkinferencenetworkgeneexpressiongeneregulationpreprocessing
2 stars 4.60 score 5 scriptsbioc
MEIGOR:MEIGOR - MEtaheuristics for bIoinformatics Global Optimization
MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow.
Maintained by Jose A. Egea. Last updated 5 months ago.
systemsbiologyoptimizationsoftware
4.12 score 44 scriptsbioc
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.
Maintained by Attila Gabor. Last updated 13 days ago.
cellbasedassayscellbiologyproteomicsnetworkinference
3.78 score 9 scriptsbioc
CNORdt:Add-on to CellNOptR: Discretized time treatments
This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.
Maintained by A. MacNamara. Last updated 5 months ago.
immunooncologycellbasedassayscellbiologyproteomicstimecourse
3.78 score 15 scriptsbioc
CNORfuzzy:Addon to CellNOptR: Fuzzy Logic
This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).
Maintained by T. Cokelaer. Last updated 5 months ago.
3.60 score 7 scripts