switchde specifications


Unique identifier OMICS_12557
Name switchde
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.6.0
Stability Stable
methods, stats, testthat, BiocStyle, SummarizedExperiment, dplyr, ggplot2, rmarkdown, knitr, tidyr, R(>=3.4), numDeriv, SingleCellExperiment
Source code URL https://codeload.github.com/kieranrcampbell/switchde/zip/master
Maintained Yes




No version available



  • person_outline kieran.campbell
  • person_outline Junhyong Kim

Additional information


Publication for switchde

switchde citation


Computational approaches for interpreting scRNA‐seq data

PMCID: 5575496
PMID: 28524227
DOI: 10.1002/1873-3468.12684

[…] in a likelihood ratio‐based fashion to identify genes which are dependent on pseudotime , .Often, we want to ask particular questions from the data, in which case parametric models are useful. In the SwitchDE method, genes which sequentially switched on or off can be identified, along with a parameter letting you learn when the switch happens . Similarly, an assumption can be that genes be describ […]

switchde institution(s)
Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK
switchde funding source(s)
Supported by a UK Medical Research Council funded doctoral studentship, a UK Medical Research Council New Investigator Research Grant (Ref. No. MR/L001411/1), the Wellcome Trust Core Award Grant Number 090532/Z/09/Z, the John Fell Oxford University Press (OUP) Research Fund and the Li Ka Shing Foundation via a OxfordStanford Big Data in Human Health Seed Grant.

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