Rose Mcgowan Bio
Bio::Graphics::Glyph::minmax is the minmax glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph is the common base class for Bio::Graphics::Glyph::graded_segments and Bio::Graphics::Glyph::xyplot. It adds an internal method named minmax() for calculating...
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Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file. SYNOPSIS use Bio::Graphics::FeatureFile; my $data = Bio::Graphics::FeatureFile->new(-file => features.txt); # create a new panel and render contents of the file onto it my $panel = $data->new_panel; my...
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Bio::DB::GFF::Feature is 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...
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Bio::Biblio is a Bibliographic Query Service module. SYNOPSIS use Bio::Biblio; my $biblio = new Bio::Biblio; print $biblio->find (perl)->get_count . "n"; my $collection = $biblio->find (brazma, authors); while ( $collection->has_next ) { print $collection->get_next; } #The new()...
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Bio::Graph::SimpleGraph is a Perl module that can create and manipulate undirected graphs. SYNOPSIS use Bio::Graph::SimpleGraph; my $graph=new SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...
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Bio::ConnectDots::SimpleGraph is a simple, hopefully fast undirected graph package. SYNOPSIS use SimpleGraph; my $graph=new Bio::ConnectDots::SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...
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Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files. SYNOPSIS use Bio::Affymetrix::CDF; # Parse the CDF file my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0}); $cdf->parse_from_file("foo.cdf"); # Find some fun facts about this chip type print...
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Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq); $aln = $in->next_aln(); This object can create...
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Bio::AlignIO::msf is a Perl module with msf sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::Align::AlignI objects to and from msf flat file databases. The rest of the documentation details each of...
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Bio::GMOD::Admin::Monitor::blat is a Perl module that can monitor a BLAT server. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $gmod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $gmod->live_version; Update a MOD installation...
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Bio::Network::IO::dip_tab is a Perl class for parsing interaction data in DIP tab-delimited format. SYNOPSIS Do not use this module directly, use Bio::Network::IO. For example: my $io = Bio::Network::IO->new(-format => dip_tab, -file => data.dip); my $network = $io->next_network; The...
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Bio::Phylo::Manual is a Perl module that contains a Bio::Phylo v.0.14 user guide. This is the manual for Bio::Phylo. Bio::Phylo is a perl5 package for phylogenetic analysis. For installation instructions, read the README file in the root directory of the distribution. The stable URL for the...
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Bio::Phylo::Treedrawer::Svg is a Perl module that creates svg tree drawings. No serviceable parts inside. This module creates a scalable vector graphic from a Bio::Phylo::Trees::Tree object. It is called by the Bio::Phylo::Treedrawer object, so look there to learn how to create tree drawings....
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Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format =>...
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Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new(); This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE)...
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Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data. SYNOPSIS use Bio::SAGE::DataProcessing; $sage = Bio::SAGE::DataProcessing->new(); # open sequence and quality files open( READS, "library.fasta" ); open( QUAL, "library.qual.fasta" ); #...
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Bio::ClusterI module is a cluster Perl interface. SYNOPSIS # see the implementations of this interface for details but # basically my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members =...
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Bio::Matrix::PSM::InstanceSite is a PSM site occurance. SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #You can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq=>TATAAT, id=>"TATAbox1",...
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Bio::MCPrimers is a Perl module to create molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller. XPORT SUBROUTINES sub find_mc_primers...
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Bio::NEXUS::CodonsBlock is a Perl module that represents CODONS block in NEXUS file. METHODS new Title : new Usage : block_object = new Bio::NEXUS::CodonsBlock(); Function: Creates a new Bio::NEXUS::CodonsBlock object Returns : Bio::NEXUS::CodonsBlock object Args :.
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