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Treefit for R - The first software for quantitative trajectory inference

This is an implementation of Treefit in R.

Treefit is a novel data analysis toolkit that helps you perform two types of analysis: 1) checking the goodness-of-fit of tree models to your single-cell gene expression data; and 2) deciding which tree best fits your data. Treefit for R can be used in conjunction with other popular software packages, such as Seurat and dynverse.

We’ll implement Monocle 3 integration soon.

Install

Debian GNU/Linux and Ubuntu

sudo -H apt install -V -y r-base libcurl4-openssl-dev
sudo -H Rscript -e 'install.packages(c("treefit"))'

macOS

brew cask install r
echo 'options(repos="https://cloud.r-project.org")' >> ~/.Rprofile
Rscript -e 'install.packages(c("treefit"))'

Windows

install.packages(c("treefit"))

Usage

The main functions are treefit::treefit() and plot():

fit <- treefit::treefit(YOUR_SINGLE_CELL_GENE_EXPRESSION_DATA)
plot(fit)

See vignette("treefit") for details.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.