Posts

How to ask for help for Bioconductor packages

tl;dr Please post your question at the Bioconductor support website https://support.bioconductor.org/ and check the posting guide http://www.bioconductor.org/help/support/posting-guide/. It’s important that you provide reproducible code and information about your R session. Recently I have been getting more questions about several packages I maintain. It’s great to see more interest from users, but at the same time most questions lack the information I need to help the users. I have also gotten most of the questions via email, which is why I am writing this post.

An alternative to the Mexico-US wall where the US would gain millions of dollars

tl;dr There is a 600 million to 2 billion USD annual market related to crossing the Mexico-US border. Allow temporary work visas (say 3 years) to take over this market and use the money to boost the US Border Patrol to build a wall of eyes, not a physical wall. President Trump of the United States of America, cc President Peña Nieto of the United Mexican States Today, Wednesday January 25th 2017, you are expected to announce your plans about building a wall between the United States and Mexico.

Easily explore a table with shinycsv

Have you ever had to explore a table with data? I believe the answer is yes for most people that work at a computer or even just use it for communicating with their friends and family. Tables of data pop up everywhere, for example in personal finance. Websites like Mint.com allow you to download your transactions in a CSV file called transactions.csv. CSV is one of the many formats for storing tables and most likely when you try to open the transactions.

Finding possible class schedules

Over the weekend my brother wanted to figure out his class schedule for the next semester. He is a veterinary medicine and zootechnology student at UNAM. For this upcoming semester there is a set of classes he has to take and each has 8 or so instructor options. The website where he finds the class times lists about 8 pre-constructed class schedules. So he normally finds one he likes quite a bit, and then manually starts checking if he can change X instructor for Y for a given class.

Federico Sánchez Rodríguez 1950-2016

Today the UNAM community at large mourns the passing of Federico Sánchez Rodríguez. He got his bachelor’s degree from the School of Chemistry - UNAM, masters and PhD degrees from Biomedicas - UNAM, postdoc from UCSF, was a member of CIFN-UNAM now called CCG-UNAM (it’s his affiliation in this 1983 paper), and worked most of his career at IBT-UNAM.

I’m sure that he made many friends, trained many students at all levels, and had a highly productive academic career as evidenced on his homepage where he lists many papers, patents, etc.

LCG-UNAM 11 years ago

This has been a busy week. I just flew in last night from #ENAR2016 and I’m getting ready for a postdoc interview tomorrow, which means that I’m also flying today. On the flight back from #ENAR2016 I started reading a book my friend John Muschelli bought for me. It’s called The Happiness Advantage by Shawn Anchor and so far I’m loving it. There are several things that it talks about that I’ve done in the past, but maybe not in the past year.

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.

Teaching a short topic to beginner R users

A couple weeks ago I was given the opportunity to teach a 1 hr 30 min slot of an introduction to R course. In the past, I’ve taught lectures for similar courses, and I ended up asking myself what would be the best short topic to teach and how to teach it. Best short topic There are two ways to answer the first question, one boring and one more interesting.

What are reasonable work hours and salary expectations for biostats/genomics careers?

My advisor recently asked me to fill a career planning document (he’ll blog about it at some point) that has lots of questions and is being very useful. Trying to fill answer all these questions has gotten me thinking about other important things for the future. Two of them being reasonable expectations for work hours and salary in a biostats/genomics academic career. I find these questions hard to answer and even hard to talk about, and if you know me, I’m a person that asks lots of questions.

Use hidden advanced arguments for user-friendly functions

As a user Imagine that you are starting to learn how to use a specific R package, lets call it foo. You will look at the vignette (if there is one), use help(package = foo), or look at the reference manual (for example, devtools’ ref man). Eventually, you will open the help page for the function(s) you are interested in using. ?function_I_want_to_use In many packages, there is a main use case that is addressed by the package.