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mfa - Bayesian inference of bifurcations in single-cell data

mfa is an R package implementing Gibbs sampling for a Bayesian hierarchichal mixture of factor analysers for inference of bifurcations in single-cell data.

Installation

mfa may be installed either via Bioconductor (coming soon) or Github:

Installation from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("mfa")

Installation from Github

devtools::install_github("kieranrcampbell/mfa", build_vignettes = TRUE)

Usage

For a cell-by-gene matrix of expression Y, MFA can be envoked via

m <- mfa(Y)

which will perform Gibbs sampling to infer pseudotimes, branch structure, and genes involved in the bifurcation.

For full usage see the package vignette:

vignette('introduction_to_mfa')

Authors

Kieran Campbell & Christopher Yau

University of Oxford