Tools for molecular neuroanatomy

This is just a quick listing of tools I often recommend to students at the Course in Molecular Neuroanatomy. They are mainly for dealing with many genes.

From slides:

• Open office
• Libre office
• Google drive
• CSV transpose tool for Expression.csv

Finding out when and where genes are expressed:

• Excross
• mouse genes as input
• returns when and where a list of genes is expressed
• find out which genes are in other Allen datasets
• wait for images to load
• reload page for new input
• HBAset
• specific expression for many genes in the 6 Allen HBA donors
• returns where a list of genes are specifically expressed
• under construction
• treeview button doesn't work right in chrome, try firefox

I made the above two so if you find them helpful or are using them for analysis then contact me for extensions and help.

Lapis

• extracting gene symbols from text
• visual xml parsing, method:
• click on the edit simultaneously button
• select gene symbol or text of interest
• copy and paste into a new file inside lapis
• copy again and paste in excel or somewhere else

VennMaster

• comparing gene lists
• making venn/Euler diagrams
• input is a text file with tab separated gene then group entries
• use a spreadsheet tool to make list, then paste into text file
• use control+c to copy genes in mac osx

Hypergeometic test or Fisher's exact test

• used to test if the overlap between two gene sets is significant

Gene ontology analysis

• GOrilla for quick analysis
• needs a list of background genes
• human
• mouse
• ErmineJ for more control of settings

Gene network

• Cytoscape
• ReactomeF1 app

Ortholog conversion, dbOrtho

• easiest to just set input+output to gene symbol

Extracting gene lists from PDF files - pdftohtml maybe useful. 

Thanks to Christos Gkogkas for suggesting I keep track of these.