knitr::opts_chunk$set(eval = FALSE)
setRepositories(ind=1:3) # needed to automatically install Bioconductor dependencies 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("stuart-lab/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:latest
To use as a base image in a new Dockerfile:
FROM timoast/signac:latest
Signac can also be installed using conda. Note that if you use conda, you should install all packages through conda rather than R itself.
conda install -c bioconda r-signac
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.
BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg19', 'EnsDb.Hsapiens.v75'))
BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg38', 'EnsDb.Hsapiens.v86'))
BiocManager::install(c('BSgenome.Mmusculus.UCSC.mm10', 'EnsDb.Mmusculus.v79'))
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