Perform initial QC on the SPE object

LieberInstitute / Visium_SPG_AD

Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.

https://research.libd.org/Visium_SPG_AD

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Perform initial QC on the SPE object #8

Closed lcolladotor closed 2 years ago

lcolladotor commented 3 years ago

Run scran/scater
Plot known marker genes or genes of interest
Plot chrM expression inside and outside of the tissue
Plot sum_umi inside and outside of the issue

These are some of the steps we've done in spatialDLPFC.

In the end we need to decide if we are dropping any spots.

lcolladotor commented 3 years ago

Filter out lowly expressed genes too.

Likely will result in a filtered SPE object.

stephaniehicks commented 2 years ago

Excited to share that @sparthib will be taking the lead on the data analysis for this project Tagging her in for this issue.

lcolladotor commented 2 years ago

We didn't make plots for "out of tissue" either, since well, it doesn't really matter for the downstream work of this project. Though it might be useful to make them later for projects like the wrinkle/QC one (for checking "spill overs": aka, expression in spots outside of tissue).

lcolladotor commented 2 years ago

Actually, there are some plots for out of tissue, but they were from the MiSeq stage and some older images (not ideal ones).

cc @shkwon17