Every six months the Bioconductor project releases it’s new version of packages. This allows developers a time window to try out new methods and test them rigorously before releasing them to the community at large. It also means that this is an exciting time 🎉. With every release there are dozens1 of new software packages. Bioconductor version 3.8 was just released on Halloween: October 31st, 2018. Thus, this is the perfect time to browse through their descriptions and find out what’s new that can be of use to your research.
To carry on our momentum from a few weeks ago from our useR!2018 remote notes blog post, this time we will be summarizing the Demystifying Data Sience 2018 conference for which you can register for free. We are just following David Robinson’s advice to blog all the time!
So what should you blog about? @drob says no matter what stage you're at in your career, you have a lot to share.
For our club meeting today we were going to summarize the Demystifying Data Science conference but we forgot that the videos are not released yet.
Oops, we'll have to postpone our blog post. We didn't read the fine print that talk recordings will be available sometime next week. Sorry about that!
— LIBD rstats club (@LIBDrstats) July 27, 2018 So we adjusted plans and decided to continue our work on the UpSetR (Gehlenborg, 2016) package by Nils Gehlenborg.
For our July 13th 2018 LIBD rstats club meeting we decided to check as much as we could the useR!2018 conference. Here’s what we were able to figure out about it in about an hour. Hopefully our quick notes will help other rstats enthusiasts, users and developers get a glimpse of the conference. Although there’s bound to me more videos and material about the conference coming out in the following days.
By Amy Peterson
Using Git Git is a version control system that allows you to track changes made to files while working on a project, either independently or in collaboration with others. It provides a way to save many different components of a project in progress, including the source code, but also the figures and data that the code produces. The importance of understanding and using Git lies in its ability to maintain an organized record of a project, also referred to as a repository or repo, as it evolves.
By Steve Semick.
What do you do when you want to use results from the literature to anchor your own analysis? When these results are in the form of an easily accessible table, such as a .csv file or .xlsx file, then it is simple enough to download them and incorporate them into your research. Often times, however, published findings are not so easy to handle. Today, we’ll go through a practical scenario on scraping an html table from a Nature Genetics article into R and wrangling the data into a useful format.
By L. Collado-Torres.
If you are working at LIBD or with large data, it’s very likely that it won’t fit in your laptop and that you’ll be using the terminal to interact with a high performance computing cluster (like JHPCE) or server. Some small edits to your bash configuration file can make your terminal experience much more enjoyable and hopefully boost your productivity. The edits described below work for any OS.
By L. Collado-Torres.
For the past 6-7 years I have been using TextMate 2 as my text editor which I’ve found useful for R code, bash, Markdown, etc. You could also look into Sublime Text or use RStudio (post about this setup coming soon).
Sometimes students are interested in this setup, which is what I’ll document here. Though I want to highlight that you can get a very similar setup using other tools.
In this blog post Leonardo Collado-Torres explains how to contribute posts to the LIBD rstats club. While some parameters are specific to this blog, you could also use this for creating your own community blog.
Install necessary tools We first need to get the appropriate tools installed in our computer.
1. R Lets start by installing the latest version of R. At the time of writing this post, that would be R 3.
Welcome to the LIBD rstats club!
A few months ago Carrie Wright and Leonardo Collado-Torres started an R + Journal club where we have been meeting every other week to talk about R packages and discuss journal articles in our field. Some examples of what we covered are tidyverse (Wickham, 2017), BiocStyle (Oleś, Morgan, and Huber, 2017) and rmarkdown (Allaire, Xie, McPherson, Luraschi, et al., 2018) presentations. We are now taking the R portion of the club to the next level.