Urja Parekh

A new issue seems to have arisen for me while executing SoupX during QC: %%R -i data -i data_tod -i genes -i cells -i soupx_groups -o out rownames(data) = genes...

integrating snRNA (from multiome dataset) with scRNA public dataset

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Hi, I tried integrating three PBMC snRNAseq data from 10X Genomics multiome datasets with two scRNA seq data from a 10X Genomics Public dataset. However, all the data from the...

Hi, I was wondering how can one potentially use the results from the somatic SNV calls to infer clones? Do you have any specific strategies for this downstream analyses? Thanks...

Germline CNV calling error: Cannot run DetermineGermlineContigPloidy due to intability to install gcnvkernel

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Hi, I tried to run DetermineGermlineContigPloidy in cohort mode and it fails: ``` 06:34:40.112 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 06:34:40.152 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression18318423026447352871.so 06:34:40.685...

Unable to use_raster function while plotting heatmap for CopyKit

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Hi, I am using CopyKit to analyze my single cell DNA data. I have merged 7 objects containing about 25k cells. I want to plot a combined heatmap for the...

Hi Tobias, I performed the Germline CNV calling pipeline on a cohort of my samples. I would like to visualize the whole genome and per chromosome CNV plot per sample...