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Hi,
I am working with single nuclear RNAseq from 10X. for snRNAseq, does it make sense to do mitochondrial filtering? I thought it probably doesn't make sense since we are working with data from nu…
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Use this preprint:
https://www.biorxiv.org/content/10.1101/742304v2
and database:
https://docs.google.com/spreadsheets/d/1En7-UV0k0laDiIfjFkdn7dggyR7jIk3WH8QgXaMOZF0/edit#gid=0
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I am using docker container of too-many-cells v0.1.5.0 for my data. The make-tree is working fine and I am happy with the results, but the gene-expression draw-tree is giving "draw-leaf error" for any…
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Chris emailed with Blue Lake and came to this conclusion:
> FYI,
> Blue has clarified how Snare RNAseq & ATACseq should be classified. In short:
>
>> They both are single nucleus assays, but fo…
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This task involves https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/twas/filter_data/filter_snps.R for which https://github.com/LieberInstitute/10xPilot_snRNAseq-human/commits/ma…
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Hi Tim,
I'm trying to integrate a merged snATACseq object with snRNAseq data, but I keep getting the following error with my own data.
```
Error in SetAssayData.ChromatinAssay(object = object,…
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Before proceeding with the plink bed file created in https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/1e1d2bb6627b06c22decdd642178bd25f9aeb42e/twas/filter_data/filter_snps.R#L51-L53, it…
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Adding this here as not everything has been documented in individual issues.
Note: 🔴 marks things that require changes in the `BASiCS` library.
- [x] Revise abstract
- [x] Revise introduction…
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Hi,
I have eight samples (AW1 to AW8), these represent four experimental groups, two biological replicates in each group (T1 to T4; T1=AW1+AW2, T2=AW3+AW4, T3=AW5+AW6, T4=AW7+AW8). I have run an int…
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Hi,
Thank you for creating this excellent tool for single cell RNA sequencing analysis. I do not quite understand why the average expression value on my dotplot starts from -1. Could anybody help me…