Christoph Champ

Random CLI tips and tricks

Christoph — Fri, 27 Apr 2012 08:40:29 +0000

This is just a random collection of #Linux #CLI commands:

Gist

Christoph — Sun, 22 Apr 2012 03:52:17 +0000

Testing my new Gist plugin:

See: My GitHub page.

Better Colour Scales

Christoph — Fri, 20 Apr 2012 07:49:39 +0000

I have been using a certain technique to bring out the differences in my data when plotting them for a long time and thought it would be useful for others if I explained the technique:

In all the colour scales, average values are represented as a light grey, while larger and smaller values are shown in progressively higher intensity colours the farther they are from average. For most scales, the values that are more than plus or minus three standard deviations from average are shown as very dark (almost black) lines.

Here is an example colour scale (as used on the GenomeAtlas, where I used to work):

#colour, #color, #plotting

axel

Christoph — Fri, 20 Apr 2012 06:12:38 +0000

In this article, I discuss axel; a command line tool similar to wget. The difference is that it is both an accelerator and it splits the file into multiple pieces.

Axel accomplishes its speed performance by opening more than one connection at a time, effectively multiplying allowable bandwidth.

agrep

Christoph — Fri, 20 Apr 2012 06:09:29 +0000

In this article, I discuss agrep (approximate grep); a “fuzzy string searching” program or command line tool for use with the Linux operating system.

agrep selects the best-suited algorithm for the current query from a variety of the known fastest (built-in) string searching algorithms, including a bitap algorithm based on Levenshtein distances.

agrep is also the search engine in the indexer program GLIMPSE. It is free for private and non-commercial use only, and belongs to the University of Arizona.

Bioinformatics wiki

Christoph — Fri, 23 Jan 2009 17:30:33 +0000

I have put together a collection of articles relating to Bioinformatics on my wiki. These articles cover techniques, tools, tutorials, etc. relating to many different areas of Bioinformatics.

See: Category:Bioinformatics.