Description
The First Software for Quantitative Trajectory Inference.
Description
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.
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.