Tool:Single cell rnaseq analysis pipeline available

Question

[datanerd]

Hi all, I have created an automated script that takes your raw files from cell ranger and creates an integrated clustered Seurat object that can be used for visualization and downstream analysis. Also- there is an visualization app available that takes the object created from the above script and plots and does all the downstream analysis with just some clicks. clustering script - https://github.com/mamtagiri/sc_ClusteringPipeline Visualization app- https://rcg.bsd.uchicago.edu/ibdgc/seurat/ Please give recommendation if any, in making the tools better for the single cell community

can also comment here - https://www.researchgate.net/post/single_cell_rnaseq_analysis_pipeline_available

Thank you all in advance!!!

[Shicheng Guo]

Did you tried to integrate pagoda2 and velocyto into your pipeline?

[datanerd]

HI Shicheng,

I haven't yet- but thats a great suggestion. Will look into it. Mamta