Bio::BioStudio::GBrowse - GBrowse interaction

BioStudio functions for interacting with GBrowse...

NOTDOCTOR/Bio-BioStudio-2.11 - 04 Dec 2015 18:59:24 GMT - Search in distribution

lib/Bio/Graphics/GBrowseFeature.pm

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

lib/Bio/DB/Sam/SamToGBrowse.pm

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

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 GMT - Search in distribution

Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

This module provides a Perl interface to the HTSlib library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across...

RISHIDEV/Bio-DB-HTS-2.7 - 03 Jan 2017 13:23:46 GMT - Search in distribution

bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3

This script uses Bio::SeqFeature::Tools::Unflattener and Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene containment hierarchies mapped for optimal display in gbrowse. The input files are assumed to be gzipped GenBank flatfiles for ref...

CJFIELDS/BioPerl-1.007001 - 06 Nov 2016 04:02:23 GMT - Search in distribution

Bio::DB::USeq - Read USeq archive database files

Bio::DB::USeq is a BioPerl style adaptor for reading USeq files. USeq files are compressed, indexed data files supporting modern bioinformatic datasets, including genomic points, scores, and intervals. More information about the format can be found a...

TJPARNELL/Bio-DB-USeq-0.23 - 09 May 2015 04:15:41 GMT - Search in distribution

FAST::Bio::Tools::GFF - A FAST::Bio::SeqAnalysisParserI compliant GFF format parser

This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces....

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 GMT - Search in distribution

lib/Bio/DB/BigBed.pm

This module provides a high-level interface to Jim Kent's BigBed files, a type of indexed genome feature database that can be randomly accessed across the network. Please see http://genome.ucsc.edu/FAQ/FAQformat.html for information about creating th...

LDS/Bio-BigFile-1.07 - 24 Feb 2012 17:20:46 GMT - Search in distribution

Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file

The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you c...

CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 GMT - 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 GMT - Search in distribution

CGI::ParamComposite - Convert .-delimited CGI parameters to Perl classes/objects

I needed this for a fairly large single-CGI script application that I was working on. It was a script that had been actively, organically growing for 4+ years, and was getting very difficult to track the undocumented 50+ CGI parameters that were bein...

ALLENDAY/CGI-ParamComposite-0.02 - 10 Oct 2004 20:20:24 GMT - Search in distribution

Bundle::GMOD - Prerequisites for GMOD applications

The Generic Model Organism Database (GMOD) project (http://www.gmod.org) is a collection of software for running a model organism database. This bundle is the minimum required for getting the schema installed in a PostgreSQL database and running the ...

SCAIN/Bundle-GMOD-1.0 - 26 Sep 2008 19:38:26 GMT - Search in distribution

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