juliendelile / antler

R package for single-cell RNA-sequencing analysis

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

antler's Issues

install failure

Just flagging up that the package fails to install via devtools::install_github("juliendelile/Antler"), as the file common_dev.R is missing. Removing the file name from the collate section of the DESCRIPTION enables me to install the package locally.

Thanks for making this package available!

package ‘ArrayBin’ is not available

Hey Julien, just wanted to let you know that Antler is failing to install as the ArrayBin package seems to have been removed from CRAN.

Can be easily solved by running this first - but thought I would let you know

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

sorry for the queistion on installation of SAGx

I have update the BiocManager to 3.13, but got the error: package ‘SAGx’ is not available for Bioconductor version '3.13'
so please tell me how I can install the package?