Estimates Pseudotimes for Single Cell Expression Data

Implements the DeLorean model (Reid & Wernisch (2016) ) to estimate pseudotimes for single cell expression data. The DeLorean model uses a Gaussian process latent variable model to model uncertainty in the capture time of cross-sectional data.


Travis-CI Build Status

R package to model time series accounting for noise in the temporal dimension. Specifically designed for single cell transcriptome experiments.

Requirements

To render the vignettes you will need a working version (> 1.12.3) of pandoc on your machine with the pandoc-citeproc filter. On Ubuntu do:

sudo apt-get install pandoc pandoc-citeproc

Installation from CRAN

Just run the following in an R session:

install.packages('DeLorean')

Installation from source

If you prefer to have the very latest version you can install DeLorean from source. If you do not already have devtools installed, then install it by running:

install.packages('devtools')

Now you can install the development version of DeLorean with:

devtools::install_github('JohnReid/DeLorean')

Documentation

Read the vignette:

vignette('DeLorean')

News

Version 1.5.0

  • Use pre-compiled models as in rstantools.
  • Rename models to remove hyphens. Backwards compatibility is conserved however.
  • Do not expose Stan functions as this is impossible when using rstantools framework.

Version 1.4.2

  • Use updated version of roxygen2.

Version 1.4.0

  • Make changes to how compiled models are cached to satisfy silly CRAN policy. Now compilation happens more often: once per model per R session.

Version 1.3.0

  • Remove filter.genes and filter.cells, (renamed to use underscores) in order to pass CRAN checks.

Version 1.2.6

  • Deprecate filter.genes and filter.cells, (renamed to use underscores).

Version 1.2.5

Version 1.2.4

Version 1.2.3

  • Update for new package versions: rstan (2.10.1) and dplyr (0.5.0).

Version 1.2.2

  • Updated code for revision of manuscript. Changed cell size normalisation strategy.

Version 1.2.1

  • Fix for sqrt(integer) bug on Solaris x86.

Version 1.2.0

  • First version submitted to CRAN.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("DeLorean")

1.5.0 by John Reid, 4 months ago


Browse source code at https://github.com/cran/DeLorean


Authors: John Reid <[email protected]>


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports rstan, rstantools, dplyr, reshape2, stringr, ggplot2, MASS, broom, coda, parallel, functional, kernlab, fastICA, seriation, lattice, memoise

Depends on methods, Rcpp

Suggests knitr, knitcitations, rmarkdown, formatR, extrafont, testthat, svglite, VGAM

Linking to BH, Rcpp, RcppEigen, rstan, StanHeaders

System requirements: GNU make


See at CRAN