oganm / braincelltypespecificgenes Goto Github PK
View Code? Open in Web Editor NEWOut of date forever!! Migrated to https://github.com/PavlidisLab/neuroExpressoAnalysis
License: GNU General Public License v2.0
Out of date forever!! Migrated to https://github.com/PavlidisLab/neuroExpressoAnalysis
License: GNU General Public License v2.0
e.g., Allen Institute says that medial habenula is part of the thalamus, not the midbrain: http://atlas.brain-map.org/atlas?atlas=2#atlas=2&plate=100883900&structure=186&x=7798.93359375&y=4024&zoom=-3&resolution=16.75&z=6
Consider the following problem:
I have a list of genes from some analysis (maybe sorted), like GWAS, some random correlation, etc. I may want to ask if this gene list is enriched for genes which are markers of a particular cell type.
Here's what we need to know to do this:
Check to see if outlying genes are expressed in cell cultures from GSE40593
Add probesets that match multiple genes by choosing the most variable one for the individual gene. Pop up a warning when you do.
This specifically seems to be a problem when multiple cell types are merged together to form larger groups. It might make sense to assure stable expression in all the subtypes that make up the cell type @ltoker
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