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...

I am used to search in the web for the vignettes of the packages, but sometimes it is useful to access the one in the computer. In this occasions you can use: vignette(package="UpSetR") # To know if there are vignettes and their name vignette("set.metadata.plots", package = "UpSetR") # Open one of the vignettes

If you are looking for improvements in your software development you might have read or heard about test, licenses, styles, quality, ... This post is aimed to explain how and which pieces work together for a related goal. I have seen lots of post for each specific tools or steps, but not so much for a list of how do you work with all (or some). Here I list some of these tools related to R packages and GitHub. I edit as I go, so if I missed something let me know and I'll update the list. Previous work Before starting writing a new piece of software as usually avoid "reinventing the wheel", so search for similar packages, I recommend using packagefinder . Which allows you to search for keywords in the existing CRAN packages. Naming When I start a project I try to identify the name with what is its goal and then I check with available . It checks github and dictionaries to suggest a name for your package or check your name Coding just typing R code - Hadley...

I have recently learned about the RV coefficient and I wanted to share it: The RV coefficient is like a correlation between several variables. In R I found so far several methods that seems to calculate it: FactoMineR::coeffRV subselect::rv.coef MatrixCorrelation::RV However the rv.coeff function from the subselect package works with only one matrix, and the coeffRV and the RV functions differ in they results. This lead me to search for its definition. All the papers mention Escoufier as the originator of these idea. The longest citation (and more relevant) can be found on a preprint , where it is mentioned the year, the author and that several of these papers are in French. In this document we can find the definition which is only followed by the RV function, in the coeffRV function the values are scaled. You can check that: RV(scale(X, scale = FALSE), scale(Y, scale = FALSE)) == coeffRV(X, Y)$rv

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...

One of my projects for the master was to investigate using data of the TCGA project. We (my teammates and me) decided to use data of the thyroid. We aimed to discover the reasons why women suffer more thyroid carcinoma than men. Distribution of samples of the TCGA dataset from the thyroid, separated by sex I don't want to repeat all the information on the report we did, you can find the work we did, you can find everything here .  The summary of the study is: Papillary Thyroid Carcinoma (PTC) is the most common type of thyroid cancer (Agrawal et al. 2014). It is more prevalent in women than men and its common diagnosis occurs between 25 and 65 years old (The Cancer Genome Atlas Accessed: 2016-06-1). The aim of our project is to study differentially expressed genes between tumor and normal samples taking into account whether there could be a gender effect on the tumorgenesis of PTC. Using data from the The Cancer Genome Atlas (Accessed: 2016-06-1) we have performed a diffe...