Single Cell RNA Seq Analysis Code
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This code is mostly R scripts to run scRNA analysis packages, with some custom built code.
The following R code contains functions to do single cell outlier detection given a set of negative control cells. The module code: File:Simple outlier model.R. The R script (sources the previous file): File:Single cell outlier analysis.R.
A script to run SCDE by Peter Kharchenko's group: File:Single cell scde analysis.R
A script to run scDD by Keegan Korthauer: File:Single cell scDD analysis.R
A script to run basic RNA-Seq PCA and clustering analysis with the Seurat package by Rahul Satija's group: File:Single cell seurat analysis.R