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Hi there, when trying to run SpaCET with these data (https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast), I am getting an error at the SpaCET.deconvolution.matched.scRNAs…
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Currently annotation calling is one of the largest bottlenecks of the pipeline. It is currently split into several rules and accompanying scripts.
Rules
- peak_Transcripts
- peak_ExonIntron
- pe…
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Hi, While reading the data processing code you gave me, I noticed that you used some preprocessed files,
such as data.feather,
anno.feather,
good_fenes_beta_score.csv,
…
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Project UUID: c4077b3c-5c98-4d26-a614-246d12c2e5d7
Project Title: Ischaemic sensitivity of human tissue by single cell RNA seq
Project Short Name: TissueStability
Submission UUID: fd52efcc-6…
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As far as I understood, to contribute a sfaira data loader the count matrices need to be already publicly available in one way or the other. How would you deal with datasets for which raw fastq files …
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After so many attempts (solved in #320), I finally generated a loom file from my count output from cellranger 10x. Nevertheless, when I examined the error log, it said "Could not retrieve index file f…
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We've recently released an open-source tool to expand the functionality of Cell Ranger to apply to other technologies. We provide a Docker container on an open-source license (see #2) which can be use…
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Hi developers,
Nice method and code/documentation! I was wondering how feasible is to apply ANANSE to single-cell multiomics data (RNA+ATAC):
- For scalability, should I pseudobulk cells by cell…
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Hi Sqjin,
Thanks for providing this package.
I am trying to compare two scRNA samples that were analysed together in Seurat and then separated by subset to extract each sample and analyse it separat…
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I'm using the example data from the documentation.
In v1.6.0 - the file `chr20.germline.vcf` does not get generated from the germline calling step.
```
${path}/src/Monopogen.py germline -a ${pa…