Documentation
A script to convert Bam alignments into a wig representation file.
A script to convert a data file to a bed file.
A script to retrieve sequences from a list of features
A script to convert a generic data file to GFF format.
A script to convert a generic data file into a wig file.
A script 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 script to collect feature information from a BioPerl SeqFeature::Store db.
A script to collect and filter annotated features from source files.
A script to collect specific, often un-annotated regions from genes.
A script to pull out overlapping features from the database.
A script to collect data in bins around a relative position.
A script to join two or more data files and concatenate rows.
A progam to manipulate tab-delimited data files.
A program to merge two or more data files by appending columns.
A script to pull out a specific list of data rows from a data file.
A script to split a data file by rows based on common data values.
A script to convert UCSC gene tables to GFF3 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/parser/ucsc.pm