/Antler

R package for single-cell RNA-sequencing analysis

Primary LanguageRGNU General Public License v3.0GPL-3.0

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