raynamharris / dissociationtest

Hippocampal transcriptomic responses to enzyme‐mediated cellular dissociation

Hi there 👋

dissociationtest's Issues

input files differ from GEO metadata

The starting data frames aren't exactly the same as what I provided to GEO. Need to resolve so that the code runs on either the local data or the data retrieved from GEO.

Make More Functions

In this repo, three .Rmd files are used to create highly similar plots that are rendered as .md files for easily visualizing the data as a report. A few of the code chucks in my workflow would be more powerful and robust if they were turned into functions.

Specially, help turning the the "DifferentialGeneExpressionAnalysis" chuck for subsetting the data to only genes that are differentially expressed by one or more comparison.

See:
Cembrowski.Rmd
Cembrowski.md
DissociationTest.Rmd
DissociationTest.md
combo.Rmd
combo.md

Recreate the Cembrowski plots

This paper (Cembrowski et al 2016) is very similar to my experiment, so I want to compare the two. Like mine, they compare hippocampal gene expression from dorsal CA1, CA3, and DG sub regions. These cells were identifed through fac sorting to isolate genetically labeled CA1 and CA3 pyramical neurons and DG granular cells.

Goals:

• I'd like to recreate the Cembrowski plots with the Cembrowski data and with my data.

The Cembrowski data is here: https://github.com/raynamharris/DissociationTest/tree/master/data/Cembrowski

The Cembrowski code is here: https://github.com/cembrowskim/hipposeq

Missing Kallisto Gather

The Kallisto Gather process is described in another repository. I think this is something that is worthy of being turned into a function for easy use across experiments.

See https://github.com/raynamharris/BehavEphyRNAseq/blob/master/markdownfiles/02b_KallistoGather.Rmd