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.
sudo -H apt install -V -y r-base libcurl4-openssl-dev
sudo -H Rscript -e 'install.packages(c("treefit"))'
brew cask install r
echo 'options(repos="https://cloud.r-project.org")' >> ~/.Rprofile
Rscript -e 'install.packages(c("treefit"))'
install.packages(c("treefit"))
The main functions are treefit::treefit()
and plot()
:
fit <- treefit::treefit(YOUR_SINGLE_CELL_GENE_EXPRESSION_DATA)
plot(fit)
See vignette("treefit")
for details.
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
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