scRNA-seq data at different time points

Question

[Bogdan]

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

[shoujun.gu]

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...

[Bogdan]

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

[Tim Padvitski]

I guess you can do (pseudo)time ordering and trajectory analysis with any of multiple tools available, e.g. Monocle, Slingshot, TSCAN... I found this tutorial that uses TSCAN quite helpful: https://bioconductor.org/books/release/OSCA/trajectory-analysis.html