dynverse

dynverse is created to support the development, execution, and benchmarking of trajectory inference methods. Check out our preprint on bioRxiv:

Wouter Saelens*, Robrecht Cannoodt*, Helena Todorov, Yvan Saeys. “A comparison of single-cell trajectory inference methods: towards more accurate and robust tools”. bioRxiv (Mar. 2018). DOI: 10.1101/276907.

*: Equal contribution

dynverse consists of several subpackages:

Package	Status	Description
dynalysis	Coming soon	Scripts to reproduce manuscript
dynwrap		Common wrapping functionality
dynmethods		Wrappers for trajectory inference methods
dyneval		Metrics and evaluation pipeline
dyngen	Coming soon	Generator of synthetic datasets
dynnormaliser		Common normalisation functionality
dyntoy		Quick generator of small toy datasets
dynplot		Common visualisation functionality
dynutils		Various common functions

Installation

Supported platforms are Linux and Mac OS X. Windows users could use Windows Subsystem for Linux in order to run these packages on a Windows machine.

Debian / Ubuntu / Linux Mint

First you need to install a few packages:

sudo apt-get install libudunits2-dev libgsl-dev libsdl1.2-dev libreadline-dev imagemagick libfftw3-dev libudunits2-dev librsvg2-dev -y

The installation of dynmethods is sped up by preinstalling several Python libraries:

sudo apt-get install python2.7-dev python3-dev python3-pip
pip3 install --user virtualenv numpy matplotlib pandas six jinja2 python-dateutil pytz pyparsing cycler tqdm python-igraph rpy2 Cython scipy statsmodels sklearn seaborn h5py anndata

Finally, you can install the dynverse packages with devtools:

install.packages("devtools")
library(devtools)
install_github("dynverse/dynwrap", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynmethods", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dyneval", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynnormaliser", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dyntoy", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynplot", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynutils", dependencies = TRUE, build_vignettes = TRUE)

Fedora / CentOS

First you need to install a few packages:

sudo dnf install openssl-devel libcurl-devel udunits2-devel libxml2-devel gsl-devel SDL2-devel readline-devel ImageMagick-c++-devel SDL-devel openblas-devel lapack-devel librsvg2-devel

The installation of dynmethods is sped up by preinstalling several Python libraries:

sudo dnf install python2-devel python3-devel python3-pip python3-matplotlib-tk
pip3 install --user virtualenv numpy matplotlib pandas six jinja2 python-dateutil pytz pyparsing cycler tqdm python-igraph rpy2 Cython scipy statsmodels sklearn seaborn h5py anndata
Rscript -e 'install.packages("udunits2", configure.args =  c(udunits2 = '--with-udunits2-include=/usr/include/udunits2'))'

Finally, you can install the dynverse packages as follows:

install.packages("devtools")
library(devtools)
install_github("dynverse/dynwrap", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynmethods", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dyneval", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynnormaliser", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dyntoy", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynplot", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynutils", dependencies = TRUE, build_vignettes = TRUE)

Mac OS X

First you will need to install the runtime binary of SDL1.2 and the development binary of SDL2 manually. Also install librsvg with brew.

The installation of dynmethods is sped up by preinstalling several Python libraries:

pip3 install --user virtualenv numpy matplotlib pandas six jinja2 python-dateutil pytz pyparsing cycler tqdm python-igraph rpy2 Cython scipy statsmodels sklearn seaborn h5py anndata

Finally, you can install the dynverse packages as follows:

install.packages("devtools")
library(devtools)
install_github("dynverse/dynwrap", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynmethods", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dyneval", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynnormaliser", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dyntoy", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynplot", dependencies = TRUE, build_vignettes = TRUE)
install_github("dynverse/dynutils", dependencies = TRUE, build_vignettes = TRUE)