Bioinformatics or B101nformatics

My experience with Bioconductor I been involved with the Bioconductor project for several years and last year I attended the BioC2019 conference in New York. It was my first time in an international conference abroad. I'm posting here my experience with the project. Pre-conference The first time I heard about Bioconductor was in 2013 when in an internship, my main goal was to analyze data from Pichia pastoris and look at the functions of the differentially expressed genes through gene ontology. I did it with topGO and other packages included in Bioconductor. Later during the master in Bioinformatics for Health Science I studied, we used several packages from Bioconductor to analyze other data (the main project is still online ). Also as part of the master thesis I also used some other packages (the thesis involved using WGCNA ) but the main question roadblock was knowing the function and what are the genes doing. So I developed a package to compare the annotation of genes accord...

If you have a package in Bioconductor and you need to change the email (say you change from university or company) it is not fast. You need to do the following: On the bioc-devel mailing list. On the support website through "edit my profile" On your BiocCredentials Send a request to the bioc-devel for updating the maintainer email for the related packages  Update the DESCRIPTION file in the release and devel branches of all the packages the email is listed in (this can be done by Bioconductor core members if you ask so in the previous point) This is because there isn't a centralized account to control the email on all these related services. It is not hard, but you could forget something. Thanks to Leonardo and Nitesh for reporting this on the mailing list

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...

If you are developing a software you might be using a version control (If not do it :). Bioconductor until 05/2017 is using svn. However it is migrating to git, meanwhile a hybrid system is provided, where one submits the project through GitHub using git control version system and internally it uses svn. Here are some experiences developing in for Bioconductor in this configuration . After following the recommendations of the configuration .git/config ends up with: [core]     repositoryformatversion = 0     filemode = true     bare = false     logallrefupdates = true [remote "origin"]     url = https://github.com/llrs/BioCor.git     fetch = +refs/heads/*:refs/remotes/origin/* [branch "master"]     remote = origin     merge = refs/heads/master [remote "bioc"]     url = https://github.com/Bioconductor-mirror/BioCor.git     ...

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...

Yesterday I received an amazing email: Congratulations, BioCor has been added to Bioconductor! Yes, I had submitted a package for the Bioconductor project at the beginning of the week. The package calculates similarities between pathways, genes and clusters of genes based on their pathways. A pathway is a group of functionally related proteins, thus this similarities calculates the functional similarity of the pathway or genes in question. If anyone is curious what the email had this was in the body (I didn't know what to expect when I knew that it would be accepted):  Hi Lluís, Congratulations, BioCor has been added to Bioconductor! Currently, the definitive location for your Bioconductor package is in our SVN repository. The following information is to help you in your role as a package maintainer. You’ll need the following credentials to maintain your package: Subversion user ID: myuser Password: mypassword Package ‘landing pages’ Every package in Bi...