Single Cell RNA Seq Analysis Code: Difference between revisions

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>YanWu
(Created page with "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...")
 
>YanWu
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This code is mostly R scripts to run scRNA analysis packages, with some custom built code.
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. [[File:simple_outlier_model.R]]
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]]

Latest revision as of 00:14, 22 May 2016

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