li-xuyang28

Issue loading h5ad/h5seurat

1

Hi, Thank you for connecting h5ad to Seurat. I am trying to analyze an extremely large scRNAseq dataset, therefore had to subset in Scanpy first then load back to Seurat,...

Writing different language to different files or chunks of file

2

Hi there, Thanks for creating such a wonderful tool! I was wondering if it is possible to write to separate txt files based on language codes, or write them into...

Is this expected run time really expected?

4

``` Loaded expression matrix of 6659 cells and 33538 genes in 10.464452981948853 seconds... Loaded 1639 TFs... starting grnboost2 using 20 processes... 0%| | 6/33538 [01:03

Issue using textcomplexity

5

Hi, Thank you for developing such a comprehensive resource for complexity computation. I am trying the package but ran into some errors, ``` Traceback (most recent call last): File "/usr/local/bin/txtcomplexity",...

Stuck at GSEA Step

10

I am following the 10X Genomics PBMC tutorial and running the wrapper function. Everything was fine until the GSEA step, it has been stuck for over 40 hours ``` 2023-04-26...

[issue] running pySCENIC on large datasets

1

I am running pySCENIC using the singularity container with scipy (aertslab-pyscenic-scanpy-0.12.1-1.9.1.sif) on a decently large dataset on a HPC, with a 150G memory and 40 cores allocation (salloc -J interact...

Hi developer/maintainer of SEACells, Thanks for your effort in bringing out this tool! I am trying to compute SEACells with a decently large scRNAseq data (~230k cells after down-sampling) on...

Dear developers/maintainers, I have used trVAE a while ago before it became part of scArches. Now I'm trying to use the scArches implementation to annotate a new unlabeled dataset. The...

RCTD for bulk to sc devonvolution

1

Dear dev team of spacexr, Thanks for maintaining the package! I am trying to use RCTD to deconvolute TCGA bulkRNAseq with a scRNAseq object as reference (instead of spatial to...