single cell RNA-seq pipeline
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6.0 years ago
Bogdan ★ 1.4k

Dear all,

please would you advise about a single-cell RNA-seq pipeline to use, that is both robust/mature and user-friendly ? thank you very much !

-- bogdan

scRNA-seq • 3.8k views
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6.0 years ago
Mike ★ 1.9k

Please have a look at following user friendly pipeline/ tools for single-cell RNA-seq data analysis...

A step-by-step workflow for low-level analysis of single-cell RNA-seq data

https://f1000research.com/articles/5-2122/v1

http://bioconductor.org/packages/devel/workflows/html/simpleSingleCell.html

List of software packages for single-cell data analysis (by Sean Davis)

https://github.com/seandavi/awesome-single-cell

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thank you Mike ! the list of available tools is very useful indeed !

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4.9 years ago
kgosche ▴ 30

Partek Flow provides a point-and-click single-cell analysis solution that is both user-friendly and robust. You can work with data from any platform and perform QA/QC, filtering, normalization, clustering, visualization, classification, statistical analysis, pathway analysis and so on. It has an online documentation site and accesible tech support team. Here is more information about its single-cell capabilities.

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A disclaimer is expected to be included when a software being discussed requires a license purchase for part or most of its functionality. This applies in case of partek flow.

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4.9 years ago

While it's not a ready-made pipeline, I strongly recommend reading up on the many different bioconductor packages that can be used to analyze scRNA-seq: https://osca.bioconductor.org/

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That's another good one that I wasn't aware of! Thanks for sharing!

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