Search results for "Bio::Map::Position"
perlop - Perl operators and precedence
In Perl, the operator determines what operation is performed, independent of the type of the operands. For example "$x + $y" is always a numeric addition, and if $x or $y do not contain numbers, an attempt is made to convert them to numbers first. Th...
RJBS/perl-5.36.0 - 28 May 2022 00:26:10 UTC - Search in distribution- perlop - Perl operators and precedence
bam2wig.pl - A program to convert Bam alignments into a wig representation file.
This program will enumerate aligned sequence tags and generate a wig, or optionally BigWig, file. Alignments may be counted and recorded in several different ways. Strict enumeration may be performed and recorded at either the alignment's start or mi...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution- Bio::ToolBox::parser::gff - parse GFF3, GTF, and GFF files
- get_relative_data.pl - A program to collect data in bins around a relative position.
GD::SVG - Seamlessly enable SVG output from scripts written using GD
GD::SVG painlessly enables scripts that utilize GD to export scalable vector graphics (SVG). It accomplishes this task by wrapping SVG.pm with GD-styled method calls. To enable this functionality, one need only change the "use GD" call to "use GD::SV...
TWH/GD-SVG-0.33 - 10 May 2009 14:39:31 UTC - Search in distribution
Data::Edit::Xml - Edit data held in the XML format.
Edit data held in the XML format. Version 20201031. The following sections describe the methods in each functional area of this module. For an alphabetic listing of all methods by name see Index....
PRBRENAN/Data-Edit-Xml-20201031 - 31 Oct 2020 23:42:40 UTC - Search in distribution
Perl6::Form - Implements the Perl 6 'form' built-in
Formats are Perl 5's mechanism for creating text templates with fixed-width fields. Those fields are then filled in using values from prespecified package variables. Unlike Perl 5, Perl 6 doesn't have a "format" keyword. Or the associated built-in fo...
DCONWAY/Perl6-Form-0.090 - 09 Jan 2019 00:23:27 UTC - Search in distribution
Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::Prim...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::PrimarySeq - Bioperl lightweight sequence object
- Bio::SimpleAlign - Multiple alignments held as a set of sequences
- Bio::Align::AlignI - An interface for describing sequence alignments.
- 5 more results from BioPerl »
Bio::SCF - Perl extension for reading and writting SCF sequence files
This module provides a perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back. Tied Methods $ob...
LDS/Bio-SCF-1.03 - 08 Jan 2010 15:40:35 UTC - Search in distribution
Bio::DB::GFF - Storage and retrieval of sequence annotation data
Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this mo...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC - Search in distribution- Bio::DB::GFF::Feature - A relative segment identified by a feature type
- Bio::DB::GFF::RelSegment - Sequence segment with relative coordinate support
Ace::Graphics::Panel - PNG graphics of Ace::Sequence::Feature objects
The Ace::Graphics::Panel class provides drawing and formatting services for Ace::Sequence::Feature objects or Das::Segment::Feature objects. Typically you will begin by creating a new Ace::Graphics::Panel object, passing it the width of the visual di...
LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 UTC - Search in distribution
SQL::Statement::Functions - built-in & user-defined SQL functions
This module contains the built-in functions for SQL::Parser and SQL::Statement. All of the functions are also available in any DBDs that subclass those modules (e.g. DBD::CSV, DBD::DBM, DBD::File, DBD::AnyData, DBD::Excel, etc.). This documentation c...
REHSACK/SQL-Statement-1.414 - 21 Oct 2020 14:46:55 UTC - Search in distribution
Bio::Cigar - Parse CIGAR strings and translate coordinates to/from reference/query
Bio::Cigar is a small library to parse CIGAR strings ("Compact Idiosyncratic Gapped Alignment Report"), such as those used in the SAM file format. CIGAR strings are a run-length encoding which minimally describes the alignment of a query sequence to ...
TSIBLEY/Bio-Cigar-1.02 - 28 Oct 2022 23:40:54 UTC - Search in distribution
pod::CONFIGURE_HOWTO
LDS/GBrowse-2.56
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15 Jan 2017 21:29:11 UTC
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- Bio::Graphics::Browser2::PadAlignment - Insert pads into a multiple alignment
- Bio::Graphics::Browser2::Plugin::RestrictionAnnotator - Generate a restriction map track in GBrowse
Boulder::Genbank - Fetch Genbank data records as parsed Boulder Stones
Boulder::Genbank provides retrieval and parsing services for NCBI Genbank-format records. It returns Genbank entries in Stone format, allowing easy access to the various fields and values. Boulder::Genbank is a descendent of Boulder::Stream, and prov...
LDS/Boulder-1.30 - 14 Dec 2002 02:06:29 UTC - Search in distribution
Bio::DB::Das::Chado - DAS-style access to a chado database
Bio::DB::Das::Chado allows DAS style access to a Chado database, getting SeqFeatureI-compliant BioPerl objects and allowing GBrowse to access a Chado database directly....
SCAIN/Bio-DB-Das-Chado-0.35a - 07 Apr 2015 23:02:17 UTC - Search in distribution
XML::Chain::Selector - selector for traversing the XML::Chain
JKUTEJ/XML-Chain-0.06
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21 Nov 2018 09:03:44 UTC
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FAST::Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::PrimarySeq - Bioperl lightweight Sequence Object
- FAST::Bio::Align::AlignI - An interface for describing sequence alignments.
- FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
- 5 more results from FAST »
Bio::CUA::CUB::Builder - A module to calculate codon usage bias (CUB) metrics at codon level and other parameters
Codon usage bias (CUB) can be represented at two levels, codon and sequence. The latter is often computed as the geometric means of the sequence's codons. This module caculates CUB metrics at codon level. Supported CUB metrics include CAI (codon adap...
FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC - Search in distribution- Bio::CUA::CUB::Calculator - A module to calculate codon usage bias (CUB) indice for protein-coding sequences
Bio::Coordinate - Modules for working with biological coordinates
Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples....
CJFIELDS/Bio-Coordinate-1.007001 - 15 Dec 2016 05:03:14 UTC - Search in distribution- Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers.
- Bio::Coordinate::GeneMapper - Transformations between gene related coordinate systems.
- Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets.
- 1 more result from Bio-Coordinate »