Bio::DB::HTS::Query - Object representing the query portion of a BAM/SAM alignment River stage one • 1 direct dependent • 1 total dependent

This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment. Methods POD ERRORS Hey! The above document had some coding errors, which are explained below: Around line 8: =over is the last thing in the document?!...

AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 GMT - Search in distribution

Bio::DB::Bam::Query - Object representing the query portion of a BAM/SAM alignment River stage one • 2 direct dependents • 2 total dependents

This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment. Methods POD ERRORS Hey! The above document had some coding errors, which are explained below: Around line 8: =over is the last thing in the document?!...

LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 GMT - Search in distribution

Bio::DB::Query::GenBank - Build a GenBank Entrez Query River stage two • 3 direct dependents • 10 total dependents

This class encapsulates NCBI Entrez queries. It can be used to store a list of GI numbers, to translate an Entrez query expression into a list of GI numbers, or to count the number of terms that would be returned by a query. Once created, the query o...

CJFIELDS/Bio-DB-NCBIHelper-1.7.6 - 07 Dec 2019 22:14:42 GMT - Search in distribution

Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies River stage two • 74 direct dependents • 79 total dependents

Do not use this class directly. See Bio::DB::QueryI and one of the implementor classes (such as Bio::DB::Query::GenBank) for information. Those writing subclasses must define _get_params() and _parse_response(), and possibly override _request_method(...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 GMT - Search in distribution

Bio::DB::Query::SqlQuery - Object representing an SQL Query River stage zero No dependents

This class inherits from Bio::DB::Query::AbstractQuery...

CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 GMT - Search in distribution

Bio::DB::SoapEUtilities::GQueryAdaptor - Handle for Entrez SOAP GlobalQuery items River stage one • 6 direct dependents • 7 total dependents

This adaptor provides an iterator ("next_query()") and other convenience functions for parsing NCBI Entrez EUtility "egquery" SOAP results....

CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 GMT - Search in distribution

Bio::Biblio - a bibliographic query service module River stage zero No dependents

This is a class whose instances can access bibliographic repositories. It allows one to query a bibliographic database (such as MEDLINE) and then to retrieve resulting citations from it. The citations are returned in an XML format which is native to ...

CDRAUG/Bio-Biblio-1.70 - 24 Mar 2013 00:19:52 GMT - Search in distribution

AlignAid - easily run sequence alignments locally or on a cluster River stage zero No dependents

AlignAid is designed to make it easy to run the sequence alignment programs Blast and cross_match. AlignAid can accept a large number of query sequences. If a compute cluster queue such as LSF or PBS is available, AlignAid can automatically split the...

DMESSINA/AlignAid-v0.0.2 - 16 Dec 2006 01:04:35 GMT - Search in distribution

DBUtils - a module for useful Database utilities River stage zero No dependents

Helper functions for achieving common DB tasks with a GeneX DB....

JASONS/Bio-Genex-2.6.0 - 06 Feb 2001 23:15:15 GMT - Search in distribution

GO::AppHandle - Gene Ontology Data API handle River stage zero No dependents

This is a module for accessing Gene Ontology data sources, e.g the GO relational database. It defines a set of methods that provide a consistent interface independent of the way the GO data is stored. For an explanation of the GO project, please visi...

SJCARBON/go-db-perl-0.04 - 21 Dec 2009 21:56:44 GMT - Search in distribution

MCE::Shared - MCE extension for sharing data supporting threads and processes River stage one • 2 direct dependents • 3 total dependents

This module provides data sharing capabilities for MCE supporting threads and processes. MCE::Hobo provides threads-like parallelization for running code asynchronously....

MARIOROY/MCE-Shared-1.871 - 13 May 2020 09:31:04 GMT - Search in distribution

get_datasets.pl - A program to collect data for a list of features River stage zero No dependents

This program will collect dataset values from a variety of sources, including features in a BioPerl Bio::DB::SeqFeature::Store database, binary wig files .wib loaded in a database using Bio::Graphics::Wiggle, bigWig files, bigBed files, Bam alignment...

TJPARNELL/Bio-ToolBox-1.67 - 09 Nov 2019 17:02:35 GMT - Search in distribution

pod::INSTALL River stage zero No dependents

LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 GMT - Search in distribution

bp_einfo - Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases). River stage zero No dependents

Command line options: -e/--email Valid email (required by NCBI policy) -d/--db/--database NCBI database to query (default = none, which shows available databases) -f/--field print out information about a specific field code (default = none) -l/--link...

CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 GMT - Search in distribution

Bio::Das - Interface to Distributed Annotation System River stage zero No dependents

Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 GMT - Search in distribution

Data::Type - robust and extensible data- and valuetype system River stage zero No dependents

A lot of CPAN modules have a common purpose: reporting if data has some "characteristics". Email::Valid is an illustrous example: reporting if a string has characteristics of an email address. The "address()" method reports this via returning 'yes' o...

MUENALAN/Data-Type-0.02.02 - 31 Dec 2009 13:48:47 GMT - Search in distribution

Boulder::Genbank - Fetch Genbank data records as parsed Boulder Stones River stage zero No dependents

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 GMT - Search in distribution

Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2 River stage zero No dependents

The BioPerl distribution from http://bioperl.org contains code and modules that may use or require additional 'external' perl modules for advanced functionality. Many of the external modules are not contained within the standard Perl distribution. Th...

CJFIELDS/Bundle-BioPerl-2.1.9 - 16 Jan 2015 20:05:40 GMT - Search in distribution

TAIR::Blast - A module to gather automated BLAST result from TAIR (http://www.arabidopsis.org/Blast/index.jsp) River stage zero No dependents

HSUREN/TAIR-Blast-1.01 - 10 Apr 2011 02:14:12 GMT - Search in distribution

XML::EasySQL - a two-way SQL/XML base class for Perl. It was written by Curtis Lee Fulton (http://fultron.net; curtisf@fultron.net). River stage zero No dependents

XML::EasySQL is a two-way SQL/XML base class for Perl. It acts as an emulsifier for the oil and water that is SQL and XML. Features: o Two-way transforms between XML and SQL data o smart SQL updates: only altered tables are updated o unlimited tree d...

CURTISF/XML-EasySQL-1.2 - 11 Jun 2004 23:46:42 GMT - Search in distribution

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