Bioconductor

Windows user space issues with installing R packages

Are you a Microsoft Windows R user? Does your Windows username include a space? Like Firstname Lastname. Then you might occassionally run into issues installing packages due to spaces. Solutions You could either re-install Windows with a username that has no spaces such as Lastname 1, but that’s probably not an easy option. Or you can: Edit your TMP and TEMP environment variables to a location with no spaces, like C:\TEMP following instructions like these ones.

CDSBMexico: remember to apply for BioC2019 travel scholarships

This blog post was first published at the CDSBMexico website. #CDSBMexico: remember to apply for BioC2019 travel scholarships!! Due date is March 15thhttps://t.co/iegG0qQzwu Let us help you! Here we give you some ideas đź’ˇWe can also give you feedback via Slack âś…#rstats #bioconductor @Bioconductor #bioc2019 #diversity #LatAm #rstatsES pic.twitter.com/EORg8d2Qxj — ComunidadBioInfo (@CDSBMexico) March 1, 2019 About 10 months ago we announced our plans to start a new community of R/Bioconductor developers in Mexico and Latin America.

R Gene Regulatory Interaction Formulator For Inquiring Networks

This blog post was written by ME Martinez-Sanchez, S Muñoz, M Carrillo, E Azpeitia, D Rosenblueth and originally posted at the CDSB blog.1 In this blog post we will describe the package rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2019) that was one of the projects developed during the TIB2018-BCDW. We hope to continue developing Griffin and rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2019). If you have ideas, suggestions or bugs, please contact us via rGriffin GitHub repo.

Latin American R/BioConductor Developers Workshop 2018

Today I’m excited to invite you to attend the Latin American R/BioConductor Developers Workshop 2018! It’ll be held in Cuernavaca, Mexico from July 30th to August 3rd, 2018. You can find the official announcement in the Bioconductor support website. Let me share with you why I’m excited about this workshop. At BioC2017, Alejandro Reyes and I talked for a while about the low representation of Latin Americans through out the years that either of us have attended the BioC meetings1.

Updating R

As you might know by now, the latest R version was recently released (R 3.4.0). That means that you are highly encouraged to update your R installation. There are several ways to do this some of which are documented in these other blog posts: Tal Galili, 2013, Kris Eberwein, 2015. You would think that it’s just a matter of downloading the latest R installer for your OS, installing it, and continuing your analysis.

Are you doing parallel computations in R? Then use BiocParallel

It’s the morning of the first day of oral conferences at #ENAR2016. I feel like I have a spidey sense since I woke up 3 min after an email from Jeff Leek; just a funny coincidence. Anyhow, I promised Valerie Obenchain at #Bioc2014 that I would write a post about one of my favorite Bioconductor packages: BiocParallel (Morgan, Obenchain, Lang, and Thompson, 2016). By now it’s on the top 5% of downloaded Bioconductor packages, so many people know about it or are unaware that their favorite package uses it behind the scenes.

Where do I start using Bioconductor?

I was recently asked where do I get started with Bioconductor? and thought this would be a good short post. What is BioC? Briefly, Bioconductor (Gentleman, Carey, Bates, and others, 2004) is an open source project that hosts a wide range of tools for analyzing biological data with R (R Core Team, 2014). These analysis tools are bundled into packages which are designed to answer specific questions or to provide key infrastructure.

Setting up your computer for bioinformatics/biostatistics and a compedium of resources

Jumping on the train set by Hilary Parker “The Setup (Part 1)" and Alyssa Frazee “my software/hardware setup”, I’m going to share my setup and hopefully add something new. They both did a great job already, so make sure you read their posts! I have some experience with all three main OS: Windows, Linux and Mac. That being said, I know some of the basic stuff for each but I surely use Google very frequently to get help.

The new visualization package for genome data in Bioconductor: ggbio

It’s been a while since I’ve been waiting for the release of a visualization package in Bioconductor. Back in 2008 I was really impressed by the power ofGenomeGraphs and I have used it in multiple occasions. Yet from both the Bioconductor Developer Meeting in Heidelberg 2010 and BioC2011 I’ve been waiting for the release of the visualization tools developed by Michael Lawrence and Tengfei Yin at Genentech. So, after a long hiatus where I didn’t browse the biocviews in Bioconductor, I found out that Lawrence and Yin released ggbio and biovizBase (it’s more of an infrastructure package for ggbio) .

Introducing Biostatistics to first year LCG students

Around two weeks ago I gave a talk via skype to the first year students from the Undergraduate Program on Genomic Sciences (LCG in Spanish) from the National Autonomous University of Mexico (UNAM in Spanish). The talk was under the context of the Introduction to Bioinformatics Seminar Series whose goal is to familiarize the new students with the bioinformatics world. It used to be a course heavy on exploring database websites, some basic theory, and lots of new concepts and algorithm names.