Advices for Single Cell analysis. Softwares to go ?

Question

[ZheFrench]

Wondering what to use to start the analysis of a public single cells project.

Libraries were prepared with Smart -Seq2 protocol. Sequencing libraries were generated and indexed from 0.25 ng of cDNA per sample using the Nextera XT DNA Library Preparation Kit.

[lieven.sterck]

perhaps not fully up-to-date anymore but still a good starting point :

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

[GenoMax]

Should be. Last update 10 days back.

[Arup Ghosh]

HumanCellAtlas Github repo has a collection of single-cell analysis pipelines.

Code: https://github.com/HumanCellAtlas/skylab Wiki: https://github.com/HumanCellAtlas/skylab/wiki/SmartSeq2-Pipeline-(v0.2.0)