Estimates Pseudotimes for Single Cell Expression Data

Implements the DeLorean model 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.


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

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

Just run the following in an R session:

install.packages('DeLorean')

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')

Read the vignette:

vignette('DeLorean')

News

  • Increase border of inducing points in sparse approximations
  • Fix further Stan bug (feature?) with square root of integers
  • Update rstan requirement to 2.12.1 from bad 2.10 version: http://andrewgelman.com/2016/07/31/stan-2-11-good-stan-2-10-bad/
  • Update for new package versions: rstan (2.10.1) and dplyr (0.5.0).
  • Updated code for revision of manuscript. Changed cell size normalisation strategy.
  • Fix for sqrt(integer) bug on Solaris x86.
  • First version submitted to CRAN.

Reference manual

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install.packages("DeLorean")

1.2.5 by John Reid, 5 months ago


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


Authors: John Reid <john.reid@mrc-bsu.cam.ac.uk>


Documentation:   PDF Manual  


MIT + file LICENSE license


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

Depends on Rcpp

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


See at CRAN