single cell RNA-seq pipeline

Question

[Bogdan]

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

Answer 1

[Mike]

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

[Bogdan]

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

Answer 2

[alireza.khodadadi.j]

https://github.com/rezakj/iCellR

Answer 3

[kgosche]

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.

[GenoMax]

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.

Answer 4

[Friederike]

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/

[Bogdan]

thanks, another resource is : https://broadinstitute.github.io/2019_scWorkshop/scrna-seq-experimental-design.html

[Friederike]

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

[Bogdan]

and a few more slides : https://github.com/rhondabacher/ISMB2019_SingleCellTutorial

Answer 5

[shoujun.gu]

check this: https://www.embopress.org/doi/10.15252/msb.20188746