Posts Tagged ‘ Software ’

R progress indicators

June 18, 2011
By

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?

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R package DOSE released

June 12, 2011
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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

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R for the web

May 27, 2011
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There is a nice R module for apache: rApache. So you can easily publish statistics.

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More Command-Line Text Munging Utilities

May 19, 2011
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More Command-Line Text Munging Utilities

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...

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Learning R — Installing Packages

May 12, 2011
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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...

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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011
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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...

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

April 11, 2011
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Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

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 ...

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Comparison of compression

April 4, 2011
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Comparison of compression

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 made me curious to know about the differences between some compression...

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RStudio Keyboard Shortcut Reference PDF

March 21, 2011
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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...

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New GenABEL Website, and more *ABEL software

March 18, 2011
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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...

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