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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 DE analyses using pseudo-bulked data #12

Closed lcolladotor closed 2 years ago

lcolladotor commented 3 years ago

Use the data from #11 and perform DE analyses. Might use pseudoBulkDGE() from https://bioconductor.org/books/release/OSCA/multi-sample-comparisons.html#putting-it-all-together which does drop lowly expressed genes as discussed at https://github.com/LieberInstitute/Visium_IF_AD/issues/11#issuecomment-910624590.

lcolladotor commented 2 years ago

Here's the link with the new OSCA book organization http://bioconductor.org/books/3.14/OSCA.multisample/multi-sample-comparisons.html#performing-the-de-analysis

lcolladotor commented 2 years ago

Replaced by newer issues. We still have to do some more models though.