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Hi,
I am using this pipeline to reanalyze some data from Illumina Novaseq PE250bp.
And I have noticed that in this paper , they sequenced at Hiseq PE250bp (McNichol, J., Berube, P., Biller, S.…
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editor preferred term: single-nuclei ATAC-seq
alternate terms: snATAC-seq
textual definition: Analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples th…
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Hi, We're getting the below error, near the end of the pipeline.
Any idea what the issue is?
Thanks
```
You provided these parameters:
YAML file: RNAseq_4-17-23.yaml
zUMIs directory: /gpfs…
gevro updated
5 months ago
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I'm starting to regularly analyze samples multiplexed with HTOs a la [Stoeckius et al](https://www.biorxiv.org/content/early/2017/12/21/237693) and multimodal CITE-seq ADTs. I have some rough ports o…
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Hi there!
Could you please instruct me in importing data generated by 10X genomics CellRanger to SINCERA?
I'm really eager to use the TF prediction function in SINCERA.
Thank you so much!
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Hi, thank you for the previous one. now I fixed it.
I am using 10x single cell data and also spatial data to run numbat.
but it shows like this.do you know what should I do?
root@aba37e368b…
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We use STAR Solo to map results of CRISPR screens, specifically at one of the steps we map guide RNA reads that we have introduced and assign them to cells . For that we generate artificial reference,…
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Hi, I met a bug when inferring cci in image-based spatial data:
```
sdm.weight_matrix(adata, l=1.2, cutoff=0.2, single_cell=True) # weight_matrix by rbf kernel
```
 in my single-cell RNA-sequencing (scRNA-seq) data. This data comes from offspring tissues…
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Hello,
I really like CellBender and have been varying the input variables to try to figure out which settings fit my institute's samples (using v0.3.0 on Windows so unfortunately no html report).
…