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FastCAR

FastCAR is an R package to remove ambient RNA from cells in droplet based single cell RNA sequencing data.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

What things you need to install the software and how to install them

Give examples

Installing

FastCAR can be install from git with the following command.

devtools::install_git("https://git.web.rug.nl/P278949/FastCAR")

Running FastCAR is quite simple. First load the library and dependencies.

library(Matrix)
library(Seurat)
library(qlcMatrix)
library(FastCAR)


cellExpressionFolder  = c("Cellranger_output/sample1/filtered_feature_bc_matrix/")
fullMatrixFolder      = c("Cellranger_output/sample1/raw_feature_bc_matrix/")

# This folder will contain the corrected cell matrix
correctedMatrixFolder = c("Cellranger_output/sample1/corrected_feature_bc_matrix")


cellMatrix     = read.cell.matrix(cellExpressionFolder)
fullMatrix     = read.full.matrix(fullMatrixFolder)

The following functions give an idea of the effect that different settings have on the ambient RNA profile

ambProfile = describe.ambient.RNA.sequence(fullCellMatrix = fullMatrix, start = 10, stop = 500, by = 10, contaminationChanceCutoff = 0.05)
plot.ambient.profile(ambProfile)

Set


emptyDropletCutoff        = 100 
contaminationChanceCutoff = 0.05

ambientProfile = determine.background.to.remove(fullMatrix, cellMatrix, emptyDropletCutoff, contaminationChanceCutoff)
cellMatrix     = remove.background(cellMatrix, ambientProfile)

Finally write the corrected cell/gene matrix to a file, this matrix can be used in Seurat the same way as any other cell/gene matrix.


write.corrected.matrix(cellMatrix, correctedMatrixFolder, ambientProfile)

End with an example of getting some data out of the system or using it for a little demo

Running the tests

Authors

Marijn Berg - Initial work

License

This project is licensed under the GPL-3 License - see the LICENSE.md file for details

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