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)

Unfortunately, two dependencies (ArrayBin and heatmap.plus) are now only accessible on CRAN archive so they must be installed manually first.

• ArrayBin

# ArrayBin requires SAGx from Bioconductor
install.packages("BiocManager")
BiocManager::install(version = "3.13")
BiocManager::install("SAGx")

devtools::install_version('ArrayBin', version = '0.2')

• heatmap.plus

devtools::install_version('heatmap.plus', version = '1.3')

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