Bio::ToolBox

Tools for querying and analysis of genomic data

This package provides a number of Perl modules and applications for working with common bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them.

Opening and saving common tab-delimited text formats
Support for BED, GFF, VCF, narrowPeak files
Scoring intervals and annotation with datasets from microarray or sequencing experiments, including ChIPSeq, RNASeq, and more
Support for Bam, BigWig, BigBed, wig, and USeq data formats
Works with any genomic annotation in GTF, GFF3, and various UCSC formats, including refFlat, knownGene, genePred and genePredExt formats

The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized Bio::Perl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with virtually any data format.

Applications

This package includes a number of production-quality, well-documented, command line applications for the advanced and novice bioinformatic analyst. These are described on the Applications page, with links therein to help documentation.

For some common scenario and real-world examples, see the Examples page. Most of these applications are used by the author on a weekly basis in production.

For an example of using this package as a basis for an epigenetic pipeline, see the Multi-Replica Macs ChIPSeq package.

Code Libraries

The Bio::ToolBox package includes a number of Perl modules with extensive documentation that can be used in custom scripts. See the Included Libraries page for a brief explanation of what is available.

Installation

Released versions can be installed from CPAN using your favorite Perl package manger. For example, using CPAN Minus

cpanm Bio::ToolBox

Manual installation is simple with the standard Module::Build incantation.

perl ./Build.PL
./Build
./Build test
./Build install

In either case, this will get you a minimal installation that will work with text files (BED, GFF, GTF, etc), but not binary files. To work with binary Bam and BigWig files, two additional external libraries must also be compiled and installed; This is not hard, and you likely already have one (possibly both) installed on your system. Most scripts should fail gently with warnings if required modules are missing. These modules are indicated as recommended rather than required in Build.PL script.

For a step-by-step instructions to get a complete installation, see the Advanced Installation guide.

For MacOS-specific installation issues, see the MacOS notes page. Even though MacOS is unix, it has its own idiosyncrasies that I’ve discovered myself, and are written here in hope that they may be helpful to someone somewhere.

Frequently Asked Questions

OK, maybe not frequently, but the FAQ page is basically a list of questions, tips, and hints that only the author knows but that may be useful for others to know.

License

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0. For details, see the full text of the license in the LICENSE.

This package is distributed in the hope that it will be useful, but it is provided “as is” and without any express or implied warranties. For details, see the full text of the license in the file LICENSE.