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)
We highly recommend using the latest Bioconductor release.
Unreleased versions of Signac can be installed from the GitHub repository using the devtools package:
Older Signac releases can be installed from the CRAN archive using devtools:
We provide docker images for Signac via dockerhub.
To pull the latest image from the command line:
To use as a base image in a new Dockerfile:
Signac can also be installed using conda. Note that if you use conda, you should install all packages through conda rather than R itself. Make sure to set up the conda channels first: http://bioconda.github.io/user/install.html#set-up-channels
It 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.