DoubletDecon

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Error in (function (side, at = NULL, labels = TRUE, tick = TRUE, line = NA, : no locations are finite

1

I got this error while executing Main_Doublet_Decon function with a particular Seurat Object. Changing the Seurat Object (another dataset) removed the error. Any clues? This is how I proceeded from...

DirtyHarry80

Improved_Seurat_Pre_Process could not find function

1

Hello all, I'm very new to coding and Seurat and everything here so my apologies in advance if this question doesn't have all the necessary coding information that one would...

rzhao0624

"Unable to perform mcl function for blacklist clustering" while using GUI

1

Hi there, I saw a similar issue opened when running the package command line, but I am running the GUI. In the console showing the current progress, I get the...

carlyrosewilling

Request: DoubletDecon Shiny - change to platform-neutral shinyFiles directory selector

1

There are currently issues with shinyDirectoryInput which relies on clunky PowerShell Scripts and Batch Files to launch a native Windows-specific directory selection dialog. This is causing DoubletDecon's "Select input file...

kmshort

Too many doublets being called

3

Hi, I am using the DoubletDecon on a Seurat v3 data following the improved seurat preprocessing steps. I have to use rho=0.7 as higher values flags an error. However, I...

piyushjo15

all connections are in use error

2

Hi, I got the following error when running DoubletDecon, could anyone give some suggestion? Thanks. Combining similar clusters... Creating synthetic doublet profiles... Step 1: Removing possible doublets... Step 2: Re-clustering...

pengyu1608

Improved_Seurat_Pre_Process: undefined columns selected

2

Hello, I ran following code `> wt1cx wt1cx[["percent.mt"]] wt1cx 500 & nFeature_RNA < 5000 & percent.mt < 10) > wt1cx wt1cx wt1cx.allgenes wt1cx wt1cx wt1cx wt1cx library(DoubletDecon) > Improved_Seurat_Pre_Process(wt1cx, num_genes=50,...

Tushar-87

The number of cores used in parallel processing is no longer set to the max available, but chosen by the user (default is 4). No UI implementation yet (if this...

pieterjanvc

Dependancies will install when `install_github` is called (including CRAN and Bioconductor packages). Code to install dependancies provided in README for convenience only. This should not be needed. See here for...

TomKellyGenetics

"Unable to perform mcl function for blacklist clustering, please try a different rhop." from black lists

11

Hi, When I ran doublet decon, after the data cleaning and preparation steps (It was very hard to mimic your custer/top50genes/counts etc data, because clear instructions weren't given), it ran...

onurdanaci