Posted on Fri 24 May 2024 in how-to • Tagged with workflows, bioinformatics, RNAseq
TLDR - Check out this github repo for the full example: https://github.com/groverj3/minimal_nextflow_samplesheet_example
I recently wrote an article regarding some of my opinions on bioinformatics workflow design. I've written workflows in several languages over the years, but at this point it seems that Nextflow has become something of …
Posted on Sat 04 May 2024 in how-to • Tagged with R, shiny, app, RNAseq, bioinformatics, data-visualization
How do you communicate results of an analysis? What tools do you use? Scientists that work in the wet lab are accustomed to firing up excel or some instrument-specific software and working with their own data. For genomics or other types of experiments in biology that result in large datasets …
Posted on Sun 21 April 2024 in how-to • Tagged with bioinformatics, data-visualization, rnaseq
One of the, if not the, most common downstream analysis task I'm asked to perform on RNAseq data is to generate the venerable "Volcano Plot." These are kind of the bioinformatics equivalent of saying "Hey! Look how much data I have!" Regardless, they are a pretty good way to quickly …
Posted on Tue 09 July 2019 in commentary • Tagged with bioinformatics, thoughts, rnaseq, workflows
When analyzing RNAseq you're faced with many possible analysis pipelines. The biggest decision you need to make is what the purpose of your experiment is. I will make the assumption that most of the time people want to determine which genes are differentially expressed between two samples, genotypes, conditions, etc …