Question: scRNA-seq data at different time points
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gravatar for Bogdan
5 weeks ago by
Bogdan1000
Palo Alto, CA, USA
Bogdan1000 wrote:

Dear all,

please may I ask about your suggestions regarding the package(s) to use for the analysis of scRNA_seq data that has been collected at different time points (1,2,3,4,5) and to infer the disease / developmental trajectories on each cell cluster ?

thanks a lot,

-- bogdan

scrna-seq • 91 views
ADD COMMENTlink modified 1 day ago by Biostar ♦♦ 20 • written 5 weeks ago by Bogdan1000

I'm doing a similar project. And I'm afraid you have to work out your own algo to analyze these data. Unless you decide to blindly use the "batch effect removal" algos to calibrate your data...

ADD REPLYlink written 4 weeks ago by shoujun.gu370

Thank you. Yes, i have been using Conos, Harmony, Seurat3 pipelines for batch correction (as outlined in Seurat wrappers) : https://github.com/satijalab/seurat-wrappers

I have came across Tempora for gene expression time series analysis, although I have not tested yet how it works on our data : https://www.biorxiv.org/content/10.1101/846907v1.full

ADD REPLYlink written 4 weeks ago by Bogdan1000
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