Archive For July 22, 2020

Getting gene attributes from biomart

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Biomart is an Ensembl service for querying and retrieving data. Here I’ll use R/Bioconductor to get gene positions for a list of genes. We basically need a mart object which encapsulates the species, host and database information. Here I’m using the US west coast mirror. This defaults to the current build (GRCh38) of the human…

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Bioconductor and Docker

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Dockerizing your bioconductor code is one way to ensure a reproducible workflow. It also enables easier deployment to cloud environments (e.g. AWS Batch) in case you want to scale your analysis. The official Bioconductor docker containers are hosted on Docker Hub. They are built with Rstudio-server installed so that you can run an interactive analysis….

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