Responsive Remote Completion

I have been using remote completion from remote boxes for a long time, as it is available in both zsh and bash. However because establishing an SSH connection is slow, the completion is not terribly useful, you spend more time waiting for it to complete than it saves in typing. However if you set up a few SSH options to keep a master connection alive and for subsequent SSH connections to use the master connection it then is very snappy.

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ZSH global aliases

Just a short post about two useful global aliases I created. ZSH global aliases are basically variables which are expanded before the command is executed. This allows them to be placed anywhere on the line, not just at the start like traditional aliases. Bash (as far as I know) does not have an analog to ZSH global aliases, but I have found them very useful.

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Stylish reports with Knitr and Bootstrap

I am pleased to announce my project for generating styled, dynamic html reports knitr_bootstrap. Here is an example of a report.

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Setting ggplot2 default color scales

ggplot2 is a very nice R plotting library, however some people do not like the default color scales for plots. You can explicitly set the color scale for each one of your plots, but a better solution would be to simply change the defaults.

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Parsing gff files with Rcpp for use with ggbio

The ggbio package is a great tool to use for visualizing next generation sequencing data. It combines the graphing power of the ggplot2 package with the biology aware data structures in bioconductor. The package includes support for plotting genes in the standard databases supplied by bioconductor, which works well for heavily studied organisms such as human and mouse.

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