In lilin-yang/glacier: Gene List Annotation, Calculation and Illustration of Enrichment in R

knitr::opts_chunk$set(
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glacier

The goal of glacier is to calculate annotation overlap statistics for gene sets. This requires three inputs:

1. A mapping from gene set names to annotations, typically in a .csv file.
2. A mapping from gene set names to gene names, typically in a .csv file.
3. A list of genes of interest.

Installation

You can install the development version of glacier from from GitHub with:

# install.packages("devtools")
devtools::install_github("lilin-yang/glacier", build_vignettes = TRUE)

Description

library(glacier)

glacier has three main types of functions:

• The import_annotations(), import_database(), import_msigdb(), process_input_text() and process_input_seurat() functions process raw data into a glacier-specific intermediate format.
• The compute() function calculates overlap statistics from the inputs.
• The plot_statistics() and plot_overlap() functions display the calculated statistics in a graph.

An example of these functions in action, as well as the supported input formats, can be seen in vignette("console", package = "glacier").

Web application

A web interface for those less familiar with R is also provided, and can be started with webstart(). A guide to using the web interface can be found in vignette("web-app", package = "glacier").

As an alternative, an instance is hosted online at shinyapps.io.

Acknowledgements

This package was inspired by, and extends the functionality of the GSEA Compute Overlaps tool.

lilin-yang/glacier documentation built on Oct. 3, 2020, 8:06 a.m.