scEiaD

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The snakefile/scripts are heavily hardcoded in two ways: - scripts are assumed to be in ~/git/massive_integrated_eye_scRNA/src/ - the working dir is occasionally hardcoded (in those above scripts mostly) to be...

davemcg

Subset Analysis

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Dive into each major "category", where category is a cell type (e.g. Cones) and re-run scVI -> clustering to find celltypes within the major cells types (for example there are...

davemcg

Trajectory

2

[slingshot](https://bioconductor.org/packages/release/bioc/html/slingshot.html)

davemcg

Calculate Velocity

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As per https://bustools.github.io/BUS_notebooks_R/velocity.html

davemcg

Is using DNTx is valuable? Not certain what the metric of "success" would be.

davemcg

Do isoform-level tx calling with well data Inspiration: https://www.biorxiv.org/content/10.1101/2020.03.05.977991v3

davemcg