Bioinformatics or B101nformatics

For some time I have been working on one topic. I am not sure if this is how it started but I fail to see other reasons. So I'll describe why I'm now working with gene sets collections. The trigger I usually try to help others in Biostars , Bioconductor , and in the StackExchange network (specially in Bioinformatics ). On one of these sites I was trying to help some person, and in one of the comments ( Jun 21 '17 ) it says: You don't build pathway maps from bioinformatics data, you build them from wet-lab experiments. And I was : " Why not? We already know (kind of) the number of genes, and we have an idea or the number of metabolites in a cell. We have many data, why can't we build pathways?" But I did a brief literature search and I couldn't find anything (if there is something let me know in the comments).   The background Let me explain why this comment got me puzzled: in my work I am usually asked what is the relevan...

Gene Set Enrichment Analysis is a test thought to find if the position of a group along a list implies some difference. The most know method is the one maintained by the Broad Institute . As it was the first widely used in biology and holds several collection of gene sets. A gene set is a collection of genes related, by either a function or an experiment, it is as fuzzy described as a pathway. In Bioconductor there is the under used tool of BiocViews , a topic for package classificacion. We can find a category for GSEAs under Software>BiologicalQuestion>GeneSetEnrichment . This category list 74 packages at the time of writing, which provide function for Gene Set Enrichment Analysis. It will be too long (and too hard for me) to describe all the packages in that category. However, it doesn't include all the packages that perform gene set enrichment. The first package for GSEA in Bioconductor one should look is GSEABase which provides with tools for reading files from...