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Bio::BioStudio::GBrowse - GBrowse interaction ++

BioStudio functions for interacting with GBrowse AUTHOR Sarah Richardson <smrichardson@lbl.gov>. FUNCTIONS add_to_GBrowse remove_from_GBrowse link_to_chromosome() link_to_feature() get_gbrowse_src_list() Given the BioStudio config hashref, return a l...

NOTDOCTOR/Bio-BioStudio-2.00 - 25 Oct 2013 00:58:08 GMT - Search in distribution

lib/Bio/Graphics/GBrowseFeature.pm ++
LDS/GBrowse-2.55 - 10 Jul 2013 14:51:25 GMT - Search in distribution

lib/Bio/DB/Sam/SamToGBrowse.pm 1 ++
LDS/Bio-SamTools-1.39   (1 review) - 29 Aug 2013 17:00:48 GMT - Search in distribution

GD::SVG - Seamlessly enable SVG output from scripts written using GD 1 ++

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

bar2wig.pl - A script to convert bar files to wig files. ++

This program will convert binary .bar files to a conventional text-based wig file, with the option to further convert to a binary bigWig format. The bar file is a Java serialized, floating-point, binary file used natively by David Nix's TiMAT2 (T2) a...

TJPARNELL/Bio-ToolBox-1.19 - 30 May 2014 03:02:05 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

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-0.22 - 27 Apr 2014 03:41:56 GMT - Search in distribution

Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser 11 ++

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....

CJFIELDS/BioPerl-1.6.923 - 18 Dec 2013 05:15:50 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. FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this...

SCAIN/Bio-DB-Das-Chado-0.34 - 28 Sep 2012 16:41:29 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

Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel ++

This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing. All methods are as described in Bio::SeqFeatureI with the following additions: The new() ...

LDS/Bio-Graphics-2.37 - 03 Jul 2013 19:32:00 GMT - Search in distribution

lib/Bio/DB/BigWigSet.pm ++

This module provides a convenient way of adding metadata to a directory of BigWig files in such a way that it appears that all the BigWig files form a single database of sequence features. The directory should be layed out so that it contains one or ...

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

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