README.md

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.



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treefit documentation built on March 22, 2021, 5:06 p.m.