ANTLER

Antler (Another transcriptome lineage explorer) is an R package providing a set of methods for analysing single-cell RNA-seq experiments.

The idea behind Antler is to perform completely unbiased and data-driven analysis to enable the discovery of novel candidate genes and transcriptomic states.

Two vignettes demonstrate how Antler can be used to:

  1. Identify, visualize and export the transcriptomic states of a dataset (Link).

  2. Build the lineage tree of a cell population differentiating over time and infer the pseudotime dynamics of gene expression (Link).

Installation

Antler can be installed from Github via the devtools package:

if (!require("devtools")) {
  install.packages("devtools")
}
devtools::install_github("juliendelile/Antler", dependencies = TRUE)

Examples

Some of the plots produced in the two vignettes include:

  • the transcriptomic summary of the cell states

  • the cell state graph enabling the pseudotime ordering of the cells.

  • the lineage tree

  • the reconstructed pseudotime dynamics of a gene