The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.

Changes for version v1.691

  • Fix critical error in script get_relative_data.pl
  • Fix prerequisite version numbers leading to build failures
  • Change a private function to a public function

Documentation

A program to convert Bam alignments into a wig representation file.
A script to calculate correlations between two datasets along the length of a feature.
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
Parser for BED-style 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