SC3

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**Describe the bug** Please provide a clear and concise description of what the bug is. **To Reproduce** Please provide the exact code that you run and ideally share your dataset...

bsamal20

rewritten parallelism to BiocParallel package

6

Hello, I have been looking at https://github.com/hemberg-lab/SC3/issues/83 and decided to rewrite the parallelism to the [BiocParallel](https://bioconductor.org/packages/release/bioc/html/BiocParallel.html) package. The reasons could be reviewed in the first bullet below. I have successfully...

gorgitko

one node produced an error: Error in ED2(data)

1

On running sc3 function, this error appears: Error in checkForRemoteErrors(val) : one node produced an error: Error in ED2(data) : Not compatible with requested type: [type=list; target=double]. Code: (sce object...

eshraaqsaeed

When I run SC3 package manual, I can't write result to the excel with `sc3_export_results_xls` function  my session information is below ``` R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit)...

UnkownNames

No gene names in export results

4

Hi there, In an older version of SC3, when I ran sc3_export_results_xls(), and I would open the "genes" tab in the excel file, and it would have a list of...

dsimps1993

Check random seed

7

Looks like the seed is changed somewhere in the code, so sometimes results cannot be reproduced...

wikiselev

each element of 'reducedDims' must be a matrix-like object with nrow equal to 'ncol(object)

1

Hello! I tried to use SC3 and this error occured: ```Error in validObject(x) : invalid class “SingleCellExperiment” object: each element of 'reducedDims' must be a matrix-like object with nrow equal...

makimenkova

Hi, I supplied a matrix with dimnames to get_marker_genes, but the returned data.frame is lacking row.names; hence I'm not sure which genes get which values. ``` markers

friedue

Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

10

Hello! I am using SC3 for clustering of pbmc single cell data which was originally a Seurat object converted to SCE. However, I have encountered the following issue... ``` pbmc

DrLucyMac

Fixed the sparse matrix issue

1

Issue was discussed here: ``` https://github.com/hemberg-lab/SC3/issues/53 ``` This is a temp fix. The correlation function ```cor``` and ```ED2``` also need regular matrix as input, and converting the sparse matrix to...

zhangguy