NAME

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

DESCRIPTION

This package provides a number of Perl modules and scripts 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

DOCUMENTATION

See the documentation page for full details.

INSTALLATION

Released versions can be installed from CPAN using your favorite Perl installer.

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 files, including Bam and BigWig files, see the details in the Installation Guide.

AUTHOR

Timothy J. Parnell, PhD
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

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 file 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.