# Differential Composition Analysis Transformed by a Similarity matrix

## Documentation for package ‘DCATS’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

create_simMat | Generate similarity matrix with uniform confusion rate to none-self clusters
dcats_GLM | A Generalised linear model based likelihood ratio testing
detect_reference | Calculate a global phi for all cell types
getPhi | Calculate a global phi for all cell types
Haber2017 | Count matrices of intestinal epithelial scRNA-seq data from three conditions
Kang2017 | Count matrices of 8 pooled lupus patient samples within two conditions
knn_simMat | Calculate stochastic transition matrix between clusters from a KNN connection matrix
multinom_EM | An EM algorithm to fit a multinomial with maximum likelihood
Ren2021 | Count matrix and metadata of a large COVID-19 scRNA-seq data cohort.
simulation | Simulated dataset with two conditions
simulator_base | Composition size simulator
svm_simMat | Calculate stochastic transition matrix between clusters from a data frame including information about clustering