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)

Current release

Development version

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")

Old versions

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'))

Docker

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:

Conda

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

Installing genome assembly and gene annotation packages

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.

Human hg19

BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg19', 'EnsDb.Hsapiens.v75'))

Human hg38

BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg38', 'EnsDb.Hsapiens.v86'))

Mouse mm10

BiocManager::install(c('BSgenome.Mmusculus.UCSC.mm10', 'EnsDb.Mmusculus.v79'))