To use Signac first make sure Bioconductor is installed:
# Install bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()
# To automatically install Bioconductor dependencies
setRepositories(ind=1:2)
install.packages("Signac")Unreleased versions of Signac can be installed from the GitHub repository using the devtools package:
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("timoast/signac", ref = "develop")Older Signac releases can be installed from the CRAN archive using devtools:
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
# replace "0.2.5" with the version that you want to install
devtools::install_version(package = 'Signac', version = package_version('0.2.5'))We provide docker images for Signac via dockerhub.
To pull the latest image from the command line:
docker pull timoast/signac:latestTo use as a base image in a new Dockerfile:
FROM timoast/signac:latestIt can also be useful (but not essential) to install species-specific packages containing genome and gene annotation information from Bioconductor.
This table from Ensembl provides a mapping of genome assembly to the corresponding gene annotation version.