Entering edit mode
This tutorial describes the tools used to access public data from the NCBI Gene Expression Omnibus and the Sequence Read Archive. Tools covered include GEOquery, GEOmetadb, and SRAdb.
http://watson.nci.nih.gov/~sdavis/tutorials/publicdatatutorial/
Hi Sean,
Is it possible to provide an updated link for this tutorial, please?
Thanks, in advance
Bw
Ruban
The tutorial was fairly old at the time it was posted (written in 2012) but if you wanted it still, it's accessible at https://web.archive.org/web/20160304020850/http://watson.nci.nih.gov/~sdavis/tutorials/publicdatatutorial/
Might be useful as far as overall strategy but very unlikely to run without modifications that catch up with changes in R and Bioconductor. Davis has moved to University of Colorado although I didn't find any updates of that talk there. He also has a github page whioch also seems to be experiencing quite a bit of link rot: https://seandavi.github.io/
Hi, Ruban.
We have presented that tutorial at most of the Bioconductor conferences in the past few years. The most recent iterations are available at https://app.orchestra.cancerdatasci.org/ along with a few dozen other workshops and tutorials. Login and then you'll have your choice of tutorials and workshops including public data workshop (very expanded from the above link).