README.md

In Dune: Improving replicability in single-cell RNA-Seq cell type discovery

Dune

Contents

• Overview
• Installation
• Demo
• Issues
• License
• Citation

Overview

Dune is an R Package that provides a parameter-free method for optimizing the trade-off between the resolutionof the clusters and their replicability across datasets. Dune method takes as input a set of clustering results on a dataset, and iteratively merges clusters within those clusterings in order to maximize their concordance.

Installation

To install the current version of Dune , you will need Bioconductor 3.11 (i.e devel version):

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Dune")

A version compatible with R 3.6 is also available with the following commands:

if(!requireNamespace("devtools", quietly = TRUE)) {
 install.packages("devtools") 
}
devtools::install_github("HectorRDB/Dune", ref = "before_bioc_release")

The installation should only take a few seconds. The dependencies of the package are listed in the DESCRIPTION file of the package. To install R and Bioconductor, please refer to the Bioconductor install page.

Issues and bug reports

Please use the github issues to submit issues, bug reports, and comments.

Demo

Start with the vignette online.

If you to look at the vignette source code, you can either run browseVignettes(package = "Dune") if you install the package from Bioconductor find the code for the vignette here

Dune documentation built on Nov. 8, 2020, 7:55 p.m.