Search results for "dist:GBrowse Bio::Graphics::Feature"
Bio::Graphics::Browser2::AuthorizedFeatureFile - Add HTTP authorization features to FeatureFile
GBrowse internal module. METHODS POD ERRORS Hey! The above document had some coding errors, which are explained below: Around line 7: =over is the last thing in the document?!...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
axt2phy.pl - convert AXT pairwise alignment files to GFF, Fasta and wig files
This program reads an AXT pairwise alignment file and creates the GFF, Fasta and binary wig files to be used for the phylogenetic glyph for the Generic Genome Browser. AXT alignment files are used by UCSC Genome Broser. A description of the AXT files...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
wiggle2gff3.pl
Use this converter when you have dense quantitative data to display using the xyplot, density, or heatmap glyphs, and too many data items (thousands) to load into GBrowse. It creates one or more space- efficient binary files containing the quantitati...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
lib/Bio/DB/SeqFeature/Store/Alias.pm
This module can be used as a wrapper around any BioPerl database that supports the get_feature_by_name() method. It allows you to dynamically override the type, source, method and display name of each feature, as well as to assign new metadata attrib...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser2::Util - Exported utilities
This package provides functions that support the Generic Genome Browser. It is not currently designed for external use. FUNCTIONS...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser::Plugin - Base class for gbrowse plugins.
This is the base class for Generic Genome Browser plugins. Plugins are perl .pm files that are stored in the gbrowse.conf/plugins directory. Plugins are activated in the gbrowse.conf/ configuration file by including them on the list indicated by the ...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser2::Markup - Markup routines for sequences in text form
This module marks up a string with HTML cascading stylesheet styles in such a way that intersecting regions contain the union of the two intersecting styles. It also handles colors in such a way that intersecting colors are added up....
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser2::Plugin - Base class for gbrowse plugins.
This is the base class for Generic Genome Browser plugins. Plugins are perl .pm files that are stored in the gbrowse.conf/plugins directory. Plugins are activated in the gbrowse.conf/ configuration file by including them on the list indicated by the ...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser2::RegionSearch - Search through multiple databases for feature matches.
This implements a feature search based on the heuristics in Bio::Graphics::Browser2::Region. The search is distributed across all local and remote databases as specified in the data source....
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser2::GFFhelper - Helps gbrowse plugins handle GFF
This modules helps process GFF prior to loading into the database and provides rollback capability for feature editors/loaders GFF help This module deals with the different GFF2 dialects and changes them to GFF3 format. It also allows conversion of B...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser2::PadAlignment - Insert pads into a multiple alignment
This is a utility module for pretty-printing the type of alignment that comes out of gbrowse, namely a multiple alignment in which each target is aligned to a reference genome without explicit pads or other spaces. For speed and ease of use, the modu...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC
Bio::Graphics::Browser2::Plugin::Spectrogram
The Spectrogram plugin builds up a spectrogram for digitized DNA sequence using the short-time fourier transform (STFT) method, adapted from classical digital signal processing methods. A sliding window of variable size and overlap is used to calcula...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC