CNORdt

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.

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

The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.

Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.

Functions for calculating and visualizing growth-rate inhibition (GR) metrics.

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.