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nicolas.descostes@embl.it – Bioinformatics Services

Bioinformatics Services

Analysis and computational expertise

The Bioinformatics Services provide analysis and computational expertise with the aim to advance research in a collaborative environment.

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Author: nicolas.descostes@embl.it

nicolas.descostes@embl.it

Dealing with subworkflows in Snakemake

Introduction Subdividing your pipeline into subworkflows is a powerful mean to achieve complex analysis. It also enables to avoid code repetition. Typically, if one has toanalyse different types of data such as ChIP-seq and RNA-seq, and then perform multi-omics data integration, it becomes handy to…


nicolas.descostes@embl.it

Very fast R packages installation with r2u

Introduction In this post, I want to test r2u, a very rapid and efficient tool to install R packages. It currently supports 19,066 and 18,921 binary packages from CRAN in “focal” and “jammy” respectively. It also supports 207 (focal) and 215 (jammy) BioConductor packages…


nicolas.descostes@embl.it

Snakemake profile 6: Using singularity containers

In the previous posts, we saw how to get started with snakemake, reduce command-line options, submit your jobs to a cluster, define resources and threads and handling memory and timeout errors. In this last post about snakemake profiles, I will show how to use singularity containers. If…






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