README.md

In bjstewart1/GenotypeMixtures: Get donors from a set of souporcell outputs and an experimental design

GenotypeMixtures

This is an R package which allows users to take the genotype calls from souporcell and stich together genotype clusters across large single cell genomics projects with multiple microfluidic channel experiments where cells are multiplexed in an overlapping mixture design.

The package aims to simplify and streamline the post-processing of experiments initially processed with the souporcell package https://github.com/wheaton5/souporcell (Heaton et al. 2020) which allows reference free clustering of cells according to genotype.

Installation

To install this package use devtools

library(devtools)
install_github('bjstewart1/GenotypeMixtures')

Vignette

A vignette is available at https://bjstewart1.github.io/GenotypeMixtures/articles/introduction.html

Dependencies

| Package | | | :--- | --- | | igraph | https://igraph.org/ | | reshape2 | https://cran.r-project.org/web/packages/reshape2/index.html| | ggplot2 | https://ggplot2.tidyverse.org/ | | pbapply | https://cran.rstudio.com/web/packages/pbapply/index.html | | ggraph | https://github.com/thomasp85/ggraph | | vcfR | https://knausb.github.io/vcfR_documentation/ |

bjstewart1/GenotypeMixtures documentation built on Aug. 27, 2022, 2:01 p.m.