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Bio::ToolBox - Tools for querying and analysis of genomic data

This package provides a number of Perl modules and scripts for workingwith common bioinformatic data. Many bioinformatic data analysis revolvesaround working with tables of information, including lists ofgenomic annotation (genes, promoters, etc.) or defined regionsof interest (epigenetic enrichment, transcription factor bindingsites, etc.). This library works with these tables and providesa 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 sequencingexperiments, 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, includingrefFlat, knownGene, genePred and genePredExt formats

See thedocumentation page for full details.

Released versions can be installedfrom CPAN using your favorite Perl installer.

Manual installation is simple with the standardModule::Build incantation.

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

In either case, this will get you a minimal installation that will work withtext files (BED, GFF, GTF, etc), but not binary files. To work with binary files,including Bam and BigWig files, see the details in theInstallation Guide.

Timothy J. Parnell, PhDHuntsman Cancer InstituteUniversity of UtahSalt Lake City, UT, 84112

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

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