Documentation
A program to convert Bam alignments into a wig representation file.
A program to convert a data file to a bed file.
A program to retrieve sequences from a list of features
A program to convert a generic data file to GFF format.
A program to convert a generic data file into a wig file.
A program to setup a SeqFeature::Store SQLite database from UCSC data
A program to print out the available feature types in a database.
A program to collect data in bins across a list of features.
A program to collect data for a list of features
A program to collect feature information from a BioPerl SeqFeature::Store db.
A program to collect and filter annotated features from source files.
A program to collect specific, often un-annotated, regions from genes.
A program to pull out overlapping features from the database.
A program to collect data in bins around a relative position.
A program to join two or more data files and concatenate rows.
A progam to manipulate tab-delimited data files.
A progam to manipulate wiggle files.
A program to merge columns of two or more data files.
A program to pull out a specific list of data rows from a data file.
A program to split a data file by rows based on common data values.
A program to convert UCSC gene tables to GFF3 or GTF annotation.
Modules
Tools for querying and analysis of genomic data
Reading, writing, and manipulating data structure
Objects representing rows in a data table
Read, Write, and Manipulate Data File Line by Line
Common functions to Bio:ToolBox::Data family
File functions to Bio:ToolBox::Data family
SeqFeature agnostic methods for working with gene models
Fast, simple SeqFeature implementation
helper interface to various database formats
parse GFF3, GTF, and GFF files
Parser for UCSC genePred, refFlat, etc formats
common utility functions for Bio::ToolBox
Provides
in lib/Bio/ToolBox/Data.pm
in lib/Bio/ToolBox/db_helper/big.pm
in lib/Bio/ToolBox/db_helper/big.pm
in lib/Bio/ToolBox/parser/ucsc.pm