Joe Daccache

Running CellChat with a large dataset

12

Hi, I am trying to run CellChat with a large dataset ~100,000 cells but the 'computeCommunProb' step repeatedly runs into memory issues. The object is already downsampled by identity class...

Loom file outdated version for loompy

2

Hi- I am trying to take Seurat objects and write loom files and use them in loompy but I have run into this error: Seurat.loom does not appead to be...

Changing Fragment object annotation style

1

Hi- I know this issue has come up in the past when people's data is not annotated in the same way as their `annotation` objects are and they have had...

clustering plot (Figure 1e)

7

Hi - I've gotten the tool up and running and it seems to be working well. However, I am trying to understand how well my genotypes are defined/separated. How can...

Recommendations for SNP array or WGS

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Hi- I am looking to run 10X Multiome (sc paired RNA & ATAC) and I want to multiplex my samples and use a SNP array or WGS to demultiplex using...

Hi - Looking to use this package to demulitplex my single cell multiome (RNA + ATAC) data containing multiple patient samples. I was wondering if you could give me advice...

`maxATAC` prepare with sc 10X ATAC

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Hi! I am trying to run maxATAC on `scATAC` data from 10X system. I am running `maxatac preapre` and pointing the function to my fragments file that ends with `.tsv.gz`...

hi - I am trying to run demuxlet on Multiome data (the atac seq reads) and have been running into large sorts of problems. The VCF and BAM needed to...