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Are raw counts available for the scRNA-seq data? From the commands history in the Seurat object, seems like the data in the "RNA" slot under assays is normalized.
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Hi!
I was following the tutorial for integrating scRNA-seq data and scATAC-seq data using the dataset provided. However, I get the following error when I run the step: atac = tfl.findNeighbors(adat…
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Good afternoon,
I am having issues with GDCPrepare with the CPTAC-3 dataset for scRNA-seq data.
I have successfully downloaded the data with
```
#Query the data
query.exp
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Hi,
I am going to use SCATS to analyze 10x scRNA-seq data. After running cellranger, I can only get one bam file containing many cells. How can I generate metafile for SCATS step2? Can you give an ex…
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Hi Michael,
Sorry for all the questions. This might be a bit naive.
I was just wondering how you went about processing the matrices outputted from the pipeline to construct a counts matrix...? …
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## Problem
Currently SODAR auto-formats strings in multiple places in a not always ideal way:
- Underscores are replaced with spaces
- Words are forced to start with a capital letter and not cont…
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Hiya,
Can Arriba be used to detect fusions in single-cell RNAseq data (e.g. Smart-seq2). I expect to see a greater number of false positives compared to bulk RNAseq, and with a lower number of read…
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I am analyzing data similar to 10X format(seekone DD_5) using TRUST4 , which is single-cell VDJ data with barcodes and UMI. The results of the TRUST4 analysis include both airr and barcode_airr tsv re…
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Dear developers,
I have a question regarding computing niche cell type composition from following tutorial.
[https://scenvi.readthedocs.io/en/latest/tutorial/MOp_MERFISH_tutorial.html](tut)
I…
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Do you have a vignette tutorial code on how to use cTRAP on Seurat or scRNA-seq data please? Thank you!