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=item L<Bio::ToolBox::Parser::ucsc>

This parses various UCSC file formats, including different refFlat, GenePred, 
and knownGene flavors. Genes, transcripts, and exons are assembled into 
hierarchical child-parent relationships as desired.

=back

=item L<Bio::ToolBox::SeqFeature>

This is a fast, lean, simple object class for representing genomic features. 
It supports, for the most part, the L<Bio::SeqFreatureI> and L<Bio::RangeI> API 
interface without the dependencies. It uses an unorthodox blessed-array object 
structure, which provides measurable improvements in memory consumption and 
speed when loading thousands of annotated SeqFeature objects (think hg19 or hg38 
annotation). 

=item L<Bio::ToolBox::GeneTools>

This is a collection of exportable functions for working with L<Bio::SeqFeatureI> 
compliant objects representing genes and transcripts. It works with objects derived 
from one of the L<"Annotation parsers"> or a L<Bio::DB::SeqFeature::Store> database. 
The functions make hard things easy, such as identifying whether a transcript is 
coding or not (is it encoded in the C<primary_tag> or C<source_tag> or GFF 
attribute or does it have C<CDS> subfeatures?), or identify the alternative exons 
or introns of a multi-transcript gene, or pull out the 5' UTR (which is likely 
not explicitly defined in the table).

=back

=head1 SCRIPTS

The BioToolBox package comes complete with a suite of high-quality production-ready 
scripts ready for a variety of analyses. Look in the scripts folder for details. 
A sampling of what can be done include the following:

=over 4

=item * Annotated feature collection and selection

=item * Data collection and scoring for features

=item * Data file format manipulation and conversion

=item * Low-level processing of sequencing data into customizable wig representation

Scripts have built-in documentation. Execute the script without any options to print 
a synopsis of available options, or add C<--help> to print the full documentation.

=back

=head2 Data conversion

Convert from generic tables to specific bioinformatic file types.

=over 4

=item L<bam2wig.pl>

Generate read or fragment coverage or point data representations of alignments.

=item L<data2bed.pl>

Convert a table containing coordinates into a properly formatted BED file.

=item L<data2wig.pl>

Convert a table of coordinates and values into a properly formatted WIG file,
including bigWig.

=item L<data2fasta.pl>

Convert a data table of coordinates and/or sequences into multi-fasta file.

=item L<data2gff.pl>

Convert a table of coordinates into a properly formatted GFF file.

=back

=head2 Feature annotation

Work with large genomic annotation feature files.

=over 4

=item L<get_features.pl>

Collect, filter, and/or convert features from a genomic feature annotation file
into another (simpler) file for use.

=item L<get_gene_regions.pl>

Collect specific gene regions that may not be explicitly annotated but inferred
from an annotation file, including introns, UTRs, alternate or common exons, etc.

=item L<get_feature_info.pl>

Collect additional information from a genomic feature annotation file for a list
of features, such as items embedded as key=value attributes in a GFF file.

=back

=head2 Data collection

Collect data, usually some sort of scores, from genomic data, including bigWig
and Bam data files among others, for a list of genomic intervals for annotation
features.

=over 4

=item L<get_datasets.pl>

General purpose single data collection of scores in a variety of methods.

=item L<get_binned_data.pl>

Collect data in a subset of bins across genomic intervals or features in a
variety of methods.