README.md

In MetaNeighbor: Single cell replicability analysis

MetaNeighbor: a method to rapidly assess cell type identity using both functional and random gene sets

MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.

Please refer to its online or pdf documentation and consider citing Crow et al (2018) Nature Communications if you find MetaNeighbor useful in your research.

Quick installation procedure

MetaNeighbor has been tested on Windows 10, MacOS Catalina 10.15 and Linux RHEL7 and is expected to run on reasonably up-to-date R (tested on versions 3.6 and 4.0). The main dependencies are the tidyverse, igraph and SingleCellExperiment libraries (full list can be found in DESCRIPTION), all missing dependencies will be automatically installed by running the following commands.

To install the stable version of MetaNeighbor, we recommend using Bioconductor:

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

To install the development version of MetaNeighbor, we recommend installing the Github version:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("gillislab/MetaNeighbor")

Installation usually completes in 1 or 2 minutes, but can take up to 20 minutes if you are starting with an empty R distribution.

MetaNeighbor demos

To run a demo of MetaNeighbor, we recommend running the vignette used for the documentation or try one of our protocols.

MetaNeighbor documentation built on Nov. 8, 2020, 5:40 p.m.