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singleron-RD / CeleScope

Single Cell Analysis Pipelines
https://www.singleron.bio/
MIT License
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Celescope needs an improved documentation/manual #278

Open wendelljpereira opened 4 months ago

wendelljpereira commented 4 months ago

We have recently acquired some of the single-cell kits from Singleron in the USA and are now ready for the data analysis.

I have to say that I do not remember ever seeing software from a commercial product with such poor documentation. There is no clear guidance on executing the analysis, what parameters can be modified, and what is happening under the hood.

Other companies that provide single-cell technologies are much better in this regard. I tried other three providers and could always run their code without issues, while am waisting time trying to figure our how to run Celescope in our server.

Best Regards, Wendell

zhouyiqi91 commented 4 months ago

Hi Wendell, Sorry for the inconvenience, celescope's documentation really needs to be improved. Assume that you need to use the rna pipeline. In celescope V1 version we need to combine each tools so here is a slightly more detailed step-by-step explanation. https://github.com/singleron-RD/CeleScope/blob/v1.15.0/docs/rna/multi_rna.md In celescope V2 version, we use STARSolo and STARsolo does all the heavy lifting (demultiplexing and error correction of barcodes and UMI, mapping, quantification), so the entire rna pipeline is basically a wrapper of STARsolo. After STARsolo generates the expression matrix, scanpy is used for clustering and dimensionality reduction. The specific code is here https://github.com/singleron-RD/CeleScope/blob/master/celescope/tools/analysis_wrapper.py Additionally, we are rewriting all pipelines in Nextflow. Hopefully this will make the workflow more transparent to users and produce better documentation. Sorry again for the inconvenience. If you have more questions about installing and running celescope, I'd be happy to answer them.

zhouyiqi91 commented 4 months ago

Hi Wendell, I just created a repo for analyzing singleron RNA data based on nf-core scrnaseq best practice, hope you find this useful. https://github.com/zhouyiqi91/scrnaseq

wendelljpereira commented 4 months ago

Hi @zhouyiqi91,

Thanks for the additional links and information. I managed to start my runs and am waiting in the outputs, but will look into the nf-core pipeline for the analysis of my next datasets.

Best Regards, Wendell