https://github.com/kevinrue/hancock
Cell signatures, with confidence.
https://github.com/kevinrue/hancock
bioconductor-package classification-algorithm machine-learning single-cell-rna-seq
Last synced: 6 months ago
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Cell signatures, with confidence.
- Host: GitHub
- URL: https://github.com/kevinrue/hancock
- Owner: kevinrue
- License: other
- Created: 2018-11-20T22:16:05.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2020-06-01T13:47:55.000Z (over 5 years ago)
- Last Synced: 2025-03-24T11:37:50.324Z (7 months ago)
- Topics: bioconductor-package, classification-algorithm, machine-learning, single-cell-rna-seq
- Language: R
- Homepage: http://kevinrue.github.io/hancock
- Size: 10.8 MB
- Stars: 9
- Watchers: 9
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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# hancock 
The goal of the [_hancock_](https://github.com/kevinrue/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`](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) class.
# Prerequisites
The [_hancock_](https://github.com/kevinrue/hancock) package supports classes of gene sets defined in multiple packages.
However, it uses `BaseSets` classes defined in the [_unisets_](https://github.com/kevinrue/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_](https://github.com/Kayla-Morrell/GeneSet) package.
This package may be installed as follows:
```
devtools::install_github("Kayla-Morrell/GeneSet")
```
# Installation
The [_hancock_](https://github.com/kevinrue/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](CONTRIBUTING.md) for more details.