Databases

Annotating KEGG compounds to pathway

To annotate a list of KEGG compounds to the KEGG pathways where they are involved I used the R package KEGGREST from Bioconductor. library(KEGGREST) So, having a list of KEGG compounds saved in a character vector like kegg_compounds, we use the method keggGet in batches of maximum 10 compounds to annotate them. The following (rudimentary) code, queries the database in batches of ten compounds fiddling a list (pathways) where it creates an entry per pathway and updates the field compounds with the compounds from kegg_compounds for each pathway.

Boston's Temperature Chart

At the end of January I will be moving to Boston. I will start my post-doc at the Boston Children’s Hospital. So… I started looking to weather and temperature conditions. I used Weather Underground to download a weatehr tamble for each month in 2016 and 2017. The aim is to create a plot with everyday mínimum and maximum temperature along all 2017. Also a heat-map indicating the weather condition of each day of the year.

Exploring public NHANES data using Rcupcake

The Rcupcake package contains functions to query different databases through the BD2K RESTful API. BD2K RESTful API is an interface that provides access to different data sources, making easier data accessibility, analysis reproducibility and scalability. The package is installed via devtools using it’s GitHub URL (hms-dbmi/Rcupcake) library( Rcupcake ) Rcupcake package follows a four-step process to retrieve the data from a database: Start session Select the variables of interest Build the JSON query Run the query to obtain the data The start.