Hi All,
I am new to this forum analyzing data from the Allen Institute, so apologies if this question is tagged wrong or otherwise naïve. On the web portal for the mouse ISH database, my query results (e.g. this one) give results over many pages. I am wondering if there is a way to download the full output of one of these comparisons from the website, or if I would only be able to access the full gene lists through the API/some other means?
Thank you in advance for your help
Hi Jacob,
Welcome to the mouse brain atlas. There is an excellent guide to accessing the data here: In Situ Hybridization (ISH) Data - How To / Allen Mouse Brain Atlas - Allen Brain Map Community Forum
-J
I appreciate you directing me to this tutorial - it provided useful context on the different functions of the ISH atlas. Where I’m having trouble right now is specifically in downloading the full, genome-wide output of my searches - I can only find the option to retrieve the XML for an individual page at a time, and cannot seem to find instructions on downloading the full output of my search query in the tutorial you linked me to. Am I missing something, or is the process of getting to this type of output more complicated?
Hi Jacob, I don’t know if you’ve figured it out yet but what worked for me was adjusting to the threshold that I wanted (2x) and then selecting the box (to check) next to the “Fold Change” in the top left of the data output. Then when clicking through each page of the data on the webpage, I found it selected those DEGs (with x>2x change). Then when downloading the xml, only those selected were downloaded.