There seem to be a few different ways to get to the RNA-seq data (the Cell Features Search Tool, the complete datasets, or even through GEO or even through BICCN , so I’m hoping someone can shed a bit of light on the best way to do the following:
For a subset of genes (~10), identify whether expression is different in inhibitory (say, all GAD-cre lines) and excitatory (e.g Emx-Cre) cells, across all brain regions. Is it possible to run such a differential comparison using the online tools? Or, do we need to work with the raw data (fpkm_table.csv?) and compute the differential expression ourselves (e.g., with DESeq)?
(This is for a project in my class, and I’d like to identify the most straightforward way for students to do this! We’re working in Python, and so any tools or pointers to work with this data in Python would be much appreciated!)