GEO-fetch - library to fetch data from GEO

GEO-fetch is a library to fetch metadata from Gene Expression Omnibus.

Adding to dependencies

add the following to you build.sbt

resolvers += "jitpack" at "https://jitpack.io"
libraryDependencies += "group.aging-research" %% "geo-fetch" % "0.1.3"

Usage in code

val key = "" //your NCBI API key (empty by default)
val f =  FetchGEO(key)
val gsm = "GSM1698568"
val g: GSM = f.getGSM(gsm, true) //get GSM
val runs: List[RunInfo] = g.runs //read SRA runs of the GSM

Usage as a console tool

You can also use it from the docker container:

docker run https://quay.io/repository/comp-bio-aging/geo-fetch