# Software

### Variable probability Bernoulli outcomes – Fast and Slow

November 1, 2012 |

I am working on a project that requires the generation of Bernoulli outcomes. Typically, I would go about this using the built in sample() function like so: This works great and is fast, even for large n. Problem is, I want to generate each sample with its own unique probability. ... [Read more...]

### Using R — A Script Introduction to R

October 17, 2012 |

To many people, R is like the Everglades. They’ve heard of it, they know it’s big and has amazing treasures deep inside. Articles in the media can make it look irresistible. But after a personal or even second hand experience …  &#16... [Read more...]

### the Art of R Programming [guest post]

January 30, 2012 |

(This post is the preliminary version of a book review by Alessandra Iacobucci, to appear in CHANCE. Enjoy [both the review and the book]!) As Rob J. Hyndman enthusiastically declares in his blog, “this is a gem of a book”. I would go even further and argue that The Art ... [Read more...]

### Using R — Easier Error Handling with try()

December 7, 2011 |

In a previous post we looked at error handling in R with the tryCatch() function and how this could be used to write Java style try-catch-finally blocks. This time we’ll look at what can be done with the try() function …   read mo... [Read more...]

### Using R — Basic error Handing with tryCatch()

December 6, 2011 |

The R language definition section on Exception Handling describes a very few basics about exceptions in R but is of little use to anyone trying to write robust code that can recover gracefully in the face of errors. In fact, …   read mo... [Read more...]

### Using R — Standalone Scripts & Error Messages

December 5, 2011 |

Open-source R is an amazing tool for statistical analysis and data visualization. Serious R gurus have found ways to do just about anything entirely within the R environment. Nevertheless, there are many of us who wish to plug R into …  &#16... [Read more...]

### Comparison of ave, ddply and data.table

October 28, 2011 |

This is a copy of a post by me on the R-statistics blog. Fortran and C programmers often say that interpreted languages like R are nice and all, but lack in terms of speed. How fast something works in R… See more › [Read more...]

### FishBASE from R

August 26, 2011 |

In lab known for its quality data collection, high-speed video style, writing the weekly blog post can be a bit of a challenge for the local code monkey. That’s right, no videos today. But lucky for me, even this group … Continue reading → [Read more...]

### WordPress WordCloud with R

August 3, 2011 |

These days one can frequently read about wordclouds created with R, initiated by the release of the wordcloud package by Ian Fellows on July 23rd. So here I am to put in my two cents. I thought about creating a wordcloud of a complete blog history, so I build a ... [Read more...]

### Now I’m R-Blogging

July 10, 2011 |

Today a lot of great mails arrived at my inbox. In one of them I was reading I’ve just added your feed to the site. Where did this mail come from? The sender of the email was Tal Galili. He is a researcher in BioStatistics at the Tel Aviv ... [Read more...]

### R progress indicators

June 18, 2011 |

Complicated calculations usually take a lot of time. So how to know the progress status to estimate how much time the program still needs to finish? [Read more...]

### R package DOSE released

June 12, 2011 |

Disease Ontology (DO) provides an open source ontology for the integration of biomedical data that is associated with human disease. DO analysis can lead to interesting discoveries that deserve further clinical investigation. DOSE was designed for semantic similarity measure and enrichment analysis. Read More: 619 Words Totally [Read more...]

### R for the web

May 27, 2011 |

There is a nice R module for apache: rApache. So you can easily publish statistics. [Read more...]

### More Command-Line Text Munging Utilities

May 19, 2011 |

In a previous post I linked to gcol as a quick and intuitive alternative to awk. I just stumbled across yet another set of handy text file manipulation utilities from the creators of the BEAGLE software for GWAS data imputation and analysis. In additio...

### Learning R — Installing Packages

May 12, 2011 |

One of the reasons to use R for analysis and visualization is the rich ecosystem of ‘packages’ contributed by others. In most cases, just as with smartphones, “There’s a package for that.” If you want to be efficient you n... [Read more...]

### PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011 |

PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f... [Read more...]

### Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

April 11, 2011 |

Lately I haven't written as many full length posts as usual, but here's a quick roundup of a few links I've shared on Twitter (@genetics_blog) over the last week:First, 23andMe is having a big DNA Day Sale (\$108) for the kit + 1 year of their personal ...

### Comparison of compression

April 4, 2011 |

I recently wrote an email with an attached LZMA archive. It was immediately answered with something like: "What are you doing? I had to boot linux to open the file!" First of all I don't care whether user of proprietary systems are able to read open formats, but this answer ... [Read more...]

### RStudio Keyboard Shortcut Reference PDF

March 21, 2011 |

I recently started using RStudio, the amazing new IDE for R. You can view all of RStudio's keyboard shortcuts by going to the help menu, but I made this printable reference for myself and thought I'd share it. I only included the Windows shortcuts, and... [Read more...]

### New GenABEL Website, and more *ABEL software

March 18, 2011 |

The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously mentioned ProbABEL R packages. There are now a handful of useful R packages and other software utilities facilita... [Read more...]
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