How do I run the BAM and CRAM download scripts?
The BAM and CRAM download scripts require wget. Once you have wget, follow the instructions at the top of the scripts.
Mac OS or Linux
wget can be obtained using homebrew on Mac OSX. Install homebrew, then type:
brew install wget
Install Cygwin. Then install the wget package.
How do I use the API?
The Application Programming Interface (API) can be used to access the CeNDR database and make a variety of queries. The API documentation details the types of queries you can make and provides examples in a variety of languages. If you are unfamiliar with APIs and how they work, I recommend taking a look at this guide.
R can be used to make queries to the API. See the examples below:
Fetch a dataframe of strain data
library(jsonlite) df <- fromJSON("https://elegansvariation.org/api/strain")
Fetch all strains for a given isotype
library(jsonlite) CB_strains <- fromJSON("https://www.elegansvariation.org/api/strain/isotype/CB4856")