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Bio-ToolBox-2.00
River stage zero No dependents

Changes for version v2.0

  • Version number change, no code changes

Documentation

bam2wig.pl
A program to convert Bam alignments into a wig representation file.
correlate_position_data.pl
A script to calculate correlations between two datasets along the length of a feature.
data2bed.pl
A program to convert a data file to a bed file.
data2fasta.pl
A program to retrieve sequences from a list of features
data2gff.pl
A program to convert a generic data file to GFF format.
data2wig.pl
A program to convert a generic data file into a wig file.
db_setup.pl
A program to setup a SeqFeature::Store SQLite database from UCSC data
db_types.pl
A program to print out the available feature types in a database.
get_binned_data.pl
A program to collect data in bins across a list of features.
get_datasets.pl
A program to collect data for a list of features
get_feature_info.pl
A program to collect feature information from a BioPerl SeqFeature::Store db.
get_features.pl
A program to collect and filter annotated features from source files.
get_gene_regions.pl
A program to collect specific, often un-annotated, regions from genes.
get_intersecting_features.pl
A program to pull out overlapping features from the database.
get_relative_data.pl
A program to collect data in bins around a relative position.
join_data_file.pl
A program to join two or more data files and concatenate rows.
manipulate_datasets.pl
A progam to manipulate tab-delimited data files.
manipulate_wig.pl
A progam to manipulate wiggle files.
merge_datasets.pl
A program to merge columns of two or more data files.
pull_features.pl
A program to pull out a specific list of data rows from a data file.
split_data_file.pl
A program to split a data file by rows based on common data values.
ucsc_table2gff3.pl
A program to convert UCSC gene tables to GFF3 or GTF annotation.

Modules

Bio::ToolBox
Tools for querying and analysis of genomic data
Bio::ToolBox::Data
Reading, writing, and manipulating data structure
Bio::ToolBox::Data::Feature
Objects representing rows in a data table
Bio::ToolBox::Data::Iterator
Class for iterating through Data tables
Bio::ToolBox::Data::Stream
Read, Write, and Manipulate Data File Line by Line
Bio::ToolBox::Data::core
Common functions to Bio:ToolBox::Data family
Bio::ToolBox::Data::file
File functions to Bio:ToolBox::Data family
Bio::ToolBox::GeneTools
SeqFeature agnostic methods for working with gene models
Bio::ToolBox::Parser
generic parsing tool for GFF, UCSC, BED
Bio::ToolBox::Parser::bed
Parser for BED-style formats
Bio::ToolBox::Parser::gff
parse GFF3, GTF, and generic GFF files
Bio::ToolBox::Parser::ucsc
Parser for UCSC genePred, refFlat, etc formats
Bio::ToolBox::Parser::ucsc::builder
Build gene and transcript SeqFeatures from UCSC formats
Bio::ToolBox::SeqFeature
Fast, simple SeqFeature implementation
Bio::ToolBox::big_helper
Bio::ToolBox::db_helper
helper interface to various database formats
Bio::ToolBox::db_helper::alignment_callbacks
Bio::ToolBox::db_helper::bam
Bio::ToolBox::db_helper::big
Bio::ToolBox::db_helper::bigbed
Bio::ToolBox::db_helper::bigwig
Bio::ToolBox::db_helper::config
Bio::ToolBox::db_helper::constants
Bio::ToolBox::db_helper::hts
Bio::ToolBox::db_helper::seqfasta
Bio::ToolBox::db_helper::useq
Bio::ToolBox::db_helper::wiggle
Bio::ToolBox::utility
common utility functions for Bio::ToolBox

Provides

Bio::ToolBox::db_helper::big::BedIteratorWrapper
in lib/Bio/ToolBox/db_helper/big.pm
Bio::ToolBox::db_helper::big::BigWigSet
in lib/Bio/ToolBox/db_helper/big.pm

Other files