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JunyueC / sci-fate_analysis

Downstream analysis script for sci-fate (TF-gene linkage analysis / cell linkage analysis)
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Can cell linkage be used with datasets lacking new expression info? #3

Open hummuscience opened 4 years ago

hummuscience commented 4 years ago

In figure 3 of the paper you show a 3D plot with timer on the z axis and UMAP1/2 on X/Y.

I understand that the analysis performed was done with the following script: https://github.com/JunyueC/sci-fate_analysis/blob/master/Main_script_cell_linkage_analysis.R

I was wondering if the same analysis/plot can be done using data from a "normal" time course experiment (for example, see Sharma et al 2020 https://www.nature.com/articles/s41586-019-1900-1?platform=oscar&draft=collection).

JunyueC commented 4 years ago

Yes - I think the same plot can be shown if you have the information about the cell state transition path at single cell level. This can be inferred by RNA velocity for normal single cell RNA-seq data.

On Jul 22, 2020, at 1:24 PM, Muad Abd El Hay notifications@github.com wrote:

In figure 3 of the paper you show a 3D plot with timer on the z axis and UMAP1/2 on X/Y.

I understand that the analysis performed was done with the following script: https://github.com/JunyueC/sci-fate_analysis/blob/master/Main_script_cell_linkage_analysis.R https://github.com/JunyueC/sci-fate_analysis/blob/master/Main_script_cell_linkage_analysis.R I was wondering if the same analysis/plot can be done using data from a "normal" time course experiment (for example, see Sharma et al 2020 https://www.nature.com/articles/s41586-019-1900-1?platform=oscar&draft=collection https://www.nature.com/articles/s41586-019-1900-1?platform=oscar&draft=collection).

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hummuscience commented 4 years ago

Will this also work if it is a time course with many days in between instead of a current snapshot of development or a continuous time course of hours (like in your paper)?

JunyueC commented 4 years ago

I guess this will be challenging as the newly synthesized mRNA or intronic reads can only be used to infer cell state dynamics across several hours shorter than a whole day

On Jul 22, 2020, at 11:56 PM, Muad Abd El Hay notifications@github.com wrote:

Will this also work if it is a time course with many days in between instead of a current snapshot of development or a continuous time course of hours (like in your paper)?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/JunyueC/sci-fate_analysis/issues/3#issuecomment-662848323, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSB5OHVC6EWHTJ37NOPI4LR47NIHANCNFSM4PFCDUXA.