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### Discussed in https://github.com/satijalab/seurat/discussions/8459
Originally posted by **An17aV0** February 12, 2024
Hello everyone!
I would like to subset my data based on the genes in t…
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look for clustering benchmark datasets (from various domains) to test the approach and put the result into the documentation)
→ Clustering benchmark papers
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Dear Dr. Li, I have encountered some problems while studying TRUST4 script commands recently. I hope to receive your guidance:
About barcoderep-filter. py, the first two lines of the report. out in m…
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Hi Alex,
I observed a phenonome when I run the new release function _Barcode and cDNA on the same mate_. You give us an example to set the readFilesIn. reads1 fastq is at the first palce and the re…
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Thank you for TRUST4 I installed it this week and ran it with some sample 10X genomics files to get a feel for what it does.
Why does the cdr3.out file have so many more lines than the report.txv fil…
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As we discussed in Teichlab/bracer#21 , when using 10X Genomics outputs, reads should be split by cell and then called their VDJ types using `bracer assembly`'s `--assembled_file` option.
I suppos…
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**Is your feature request related to a problem? Please describe.**
Embeddable views of Cell Ranger HTML summary page on GigaDB. Cell Ranger is a set of analysis pipelines developed by 10X Genomics th…
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From the meta data `hf://datasets/MahmoodLab/hest/HEST_v1_0_2.csv`, I can't find the [Xenium data](https://www.10xgenomics.com/datasets/xenium-ffpe-human-breast-with-custom-add-on-panel-1-standard) pu…
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Hi,
I ran cite-seq count on cell hashing data using the whitelist from the cellranger filtered output. Since it's 10X V3 data, I mapped the cellranger filtered output barcodes to the 10X genomics w…
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Hi,
I was wondering how/if I can choose EM algorithm or the "simpler" multimapping option that distributes reads evenly across genes when using kb to count reads. And because my experiment was done…