EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

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Tips for running in windows?

RobertWhitener opened this issue · comments

Hi,

I'm currently working on scRNAseq analysis using RStudio on Windows, R v4.0.5. and am seeing some clusters that appear to be made up of cells with features from other clusters, and am trying to rule out the possibility that these are doublets, hence my interest in using DoubletDecon.

The data is comprised of FACS-sorted, well-based Smart-Seq2, paired-end 100bp reads. In total, ~5,500 cells pass basic QC, and the expression data is log-normalized and clustered using Seurat v4.

I am already familiar with Shiny, and I have installed and updated all required packages for DoubletDecon. However, I have been unable to get the DD Gui to work properly.

I can't seem to assign an input/output directory in the GUI a 'path_x' value is created in my R session whenever I try to assign the directory:

> path_x
[1] "Processing -File 'C:\\Users\\Robert' failed because the file does not have a '.ps1' extension. Specify a valid Windows PowerShell script file name, and then try again."
[2] "Windows PowerShell"                                                                                                                                                     
[3] "Copyright (C) Microsoft Corporation. All rights reserved."                                                                                                              
[4] ""                                                                                                                                                                       
[5] "Try the new cross-platform PowerShell https://aka.ms/pscore6"                                                                                                           
[6] "" 

But if I skip that step, I am able to load my Seurat Object without issue... however, whenever I set the paramaters and click one of the options at the bottom, I get this in the console:

Error in gzfile: invalid 'description' argument  3: runApp
  2: runUrl
  1: shiny::runGist

Any thoughts?

I've tried running

Improved_Seurat_Pre_Process(OBJECT, num_genes = 50, write_files = TRUE)

But I'm honestly not sure what do to with the three files that are created after this step.

Any help is appreciated!

Robert