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My journey with Bioconductor

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-conferenceThe 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 according to w…
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Sequencing: From the wet lab to the dry lab

Here I'll share some experiences for sequencing samples by RNA. Most of them will be useful for other techniques and also for single cell sequencing (or scRNA-seq). Here I'm assuming that you do a short-sequence technique from Illumina or similar companies. Also I'll provide some tips to make easier the life of the bioinformatician that will analyse the data.

Don't expect to find how many reads for sample you need or which design is better or which machine. Neither I will talk about prices or provide a list of companies and scientific platforms to look for. I won't cover how to analyse the data, or compare pipelines to process RNA-seq. Hope this post is more practical than all that but less technical.

Before sending: Get ready
You carried out your experiments and have already extracted the RNA from patients, mice, rats, cell cultures or whatever are you studying. You have them named with sensible names for your experiment like A+B-, 4789/Diff, 256-w046 and usuall…

Reviewing a preprint

After a while I write back to comment about the preprint: "Benchmarking joint multi-omics dimensionality reduction approaches for cancer study". First, I'll explain why I comment here: On 20th September 2019 I saw on twitter a poster about multiomics mentioing RGCCA, which I have been using for a while. After asking somehting about it the first author of the poster commented that would notify me when the preprint would be ready. Now that the preprint is ready, the first author of the paper, Laura, asked for comments on the preprint.


Abstract

Already from the abstract one notices that there is an special emphasis on reproducible research. The methods used and how other readers can use them, can be easily accessed and reused.

Background

The integrations methods are classified after explaining why the integration methods are needed, and why do we need to compare them.  One of these classifications are the dimension reduction approaches, which this article focus on. How…

Updating your mail on Bioconductor

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

Accessing the vignettes

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