Miscellaneous bioinformatics scripts written by me for myself and other people.
Some are fully documented, polished applications exported from a purging of Bio::ToolBox at version 1.40. These no longer fit the intent of the original package, but are too useful to discard.
Some are quickie one-off scripts thrown together for some specific need. Most illustrate the utility of using the Bio::ToolBox libraries, so if you need some inspiration....
Mostly (all?) are Perl scripts based on Bio::ToolBox, available at https://github.com/tjparnell/biotoolbox.
These scripts do not need to be installed anywhere special. They can be run
most anywhere. Most require certain Perl modules to be installed, for
example the Bio::ToolBox libraries found at this Repository. As long as
modules are installed in a PERL5 library available to your Perl installation
(either the site directory or through local::lib), they should run.
Scripts will not run if required modules are missing. You can install
missing modules using your favorite CPAN utility.
The scripts are organized into the following folders based loosely on their function.
Scripts that are about working with genomic annotation, derived either from a file or from a database.
Scripts for working with bam files. Requires installation of Bio::DB::Sam.
Scripts for working with ChIPSeq data.
Scripts for working with k-means cluster data files.
Scripts for working with tab-delimited text data tables using the
Bio::ToolBox libraries.
Scripts for working with MNase Sequencing of nucleosomes.
Scripts for customizing Best Practical's Request Tracker software.
Scripts for working with genomic sequence.
Scripts for working with somatic variant calling. Demonstrates use of working with VCF files.
Scripts for working with and manipulating wig files.
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