The goal of the hancock package is to provide a collection of methods for learning and applying gene signatures associated with cellular phenotypes and identities. Particular focus is given to single-cell data stored in objects derived from the SummarizedExperiment class.

Prerequisites

The hancock package supports classes of gene sets defined in multiple packages. However, it uses BaseSets classes defined in the unisets package to return newly learned signatures with accompanying metadata. This dependency may be installed as follows:

install.packages("devtools")
devtools::install_github("kevinrue/unisets", build_opts = c("--no-resave-data", "--no-manual"))

Several functions support the tbl_geneset class defined in the GeneSet package. This package may be installed as follows:

devtools::install_github("Kayla-Morrell/GeneSet")

Installation

The hancock package may be installed as follows:

install.packages("devtools")
devtools::install_github("kevinrue/hancock")

To build the vignette as well, please use the following code:

devtools::install_github("kevinrue/hancock", build_opts = c("--no-resave-data", "--no-manual"))

Usage

Demonstration notebooks are available as vignettes and on the companion repository: https://github.com/kevinrue/hancock2018

Contributing

Considerate contributions are very welcome! Please refer to the contributing guidelines for more details.