Search results for "Bio::DB::SeqFeature::Segment"
Bio::DB::SeqFeature::Segment - Location-based access to genome annotation data
The segment object simplifies access to Bio::DB::SeqFeature store by acting as a placeholder for a region of the genome. You can replace this statement: @features = $db->features(-seq_id=>'Chr1', -start=>5000, -end=>6000, -types=>['mRNA','match','rep...
CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution- Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
- Bio::DB::SeqFeature::Store::DBI::Pg - PostgreSQL implementation of Bio::DB::SeqFeature::Store
- Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store
- 13 more results from Bio-DB-SeqFeature »
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 USeq software package...
TJPARNELL/Bio-DB-USeq-0.26 - 24 Sep 2022 02:31:45 UTC - Search in distribution
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 - Search in distribution- pod::CONFIGURE_HOWTO
- Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store
- DAS::GUS::Segment::Feature
- 3 more results from GBrowse »
get_datasets.pl - A program to collect data for a list of features
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-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution- correlate_position_data.pl - A script to calculate correlations between two datasets along the length of a feature.
- Bio::ToolBox::Data - Reading, writing, and manipulating data structure
- Bio::ToolBox::Data::Feature - Objects representing rows in a data table
- 1 more result from Bio-ToolBox »
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/CRAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information a...
AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 UTC - Search in distribution
Bio::DB::Sam - Read SAM/BAM database files
This module provides a Perl interface to the libbam 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...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC - Search in distribution
Bio::Das::Feature - A genomic annotation
A Bio::Das::Segment::Feature object contains information about a feature on the genome retrieve from a DAS server. Each feature -- also known as an "annotation" -- has a start and end position on the genome relative to a reference sequence, as well a...
LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 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
Bio::DB::GFF::Feature - A relative segment identified by a feature type
Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherit...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC - 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 UTC - Search in distribution
Bio::Graphics::Glyph::segments - The "segments" glyph
This glyph is used for drawing features that consist of discontinuous segments. Unlike "graded_segments" or "alignment", the segments are a uniform color and not dependent on the score of the segment. METHODS This module overrides the maxdepth() meth...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution- Bio::Graphics::Glyph::whiskerplot - The whiskerplot glyph
- Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file