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.

How to release

Bump Version: in DESCRIPTION.

Add a release note to NEWS.md. You need to run Rscript -e "devtools::spell_check() after it. You may need to update inst/WORDLIST too.

Check on local:

Rscript -e "roxygen2::roxygenise()"
Rscript -e "rcmdcheck::rcmdcheck(args=c('--as-cran'), error_on='warning', check_dir='check')"

Check on win-builder.r-project.org:

rake check:win_builder

Update cran-comments.md.

Submit to CRAN:

rake cran:submit

Update document after the submission is accepted:

rake release

Update version in docs/_config.yml.

Tag:

rake tag