Search results for "Bio::Symbol::Symbol"
Tutorial - Hands-on tutorial for using Bio::NEXUS module.
Tutorial to get started using Bio::NEXUS module. INTRODUCTION The NEXUS file format standard of Maddison, et al. (1997) is designed to represent sets of data, including character data (e.g., molecular sequence alignments, morphological character sets...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC - Search in distribution
Data::Edit::Xml - Edit data held in the XML format.
Edit data held in the XML format. Version 20201031. The following sections describe the methods in each functional area of this module. For an alphabetic listing of all methods by name see Index....
PRBRENAN/Data-Edit-Xml-20201031 - 31 Oct 2020 23:42:40 UTC - Search in distribution
perlop - Perl operators and precedence
In Perl, the operator determines what operation is performed, independent of the type of the operands. For example "$x + $y" is always a numeric addition, and if $x or $y do not contain numbers, an attempt is made to convert them to numbers first. Th...
RJBS/perl-5.36.0 - 28 May 2022 00:26:10 UTC - Search in distribution- perlop - Perl operators and precedence
bp_genbank_ref_extractor - Retrieves all related sequences for a list of searches on Entrez gene
This script searches on *Entrez Gene* database and retrieves not only the gene sequence but also the related transcript and protein sequences. The gene UIDs of multiple searches are collected before attempting to retrieve them so each gene will only ...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC - Search in distribution
GO::AppHandle - Gene Ontology Data API handle
This is a module for accessing Gene Ontology data sources, e.g the GO relational database. It defines a set of methods that provide a consistent interface independent of the way the GO data is stored. For an explanation of the GO project, please visi...
SJCARBON/go-db-perl-0.04 - 21 Dec 2009 21:56:44 UTC - Search in distribution
FortyTwo::Manual - User Guide for Forty-Two
DBAURAIN/Bio-MUST-Apps-FortyTwo-0.213470
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13 Dec 2021 23:13:33 UTC
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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
process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the "correct" version of the GFF format. To use this script, download the whole genome FASTA file and save it to disk....
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC - Search in distribution
bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the "correct" version of the GFF format. To use this script, download the whole genome FASTA file and save it to disk....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SimpleAlign - Multiple alignments held as a set of sequences
- Bio::Root::Utilities - general-purpose utilities
- Bio::SeqIO::swiss - Swissprot sequence input/output stream
- 9 more results from BioPerl »
FAST::Bio::UnivAln - Bioperl alignment object
This module is the FAST::Bio::UnivAln alignment object which is part of the Bioperl project. Currently it has some nice methods for accessing an alignment after reading it in from certain formats, incl. utilities like consensus and reverse complement...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
- FAST::Bio::SeqIO::chadoxml - chadoxml sequence output stream
- FAST::Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
- 6 more results from FAST »
Bio::ConnectDots::SimpleGraph
This is a simple, hopefully fast undirected graph package. The only reason this exists is that the standard CPAN Graph pacakge, Graph::Base, is seriously broken. The package implements a small and eclectic assortment of standard graph algorithms that...
DBURDICK/Bio-ConnectDots-1.0.2 - 07 Apr 2005 22:06:44 UTC - Search in distribution- Bio::ConnectDots::ConnectDots - Top level class for 'connect-the-dots'
- Bio::ConnectDots::ConnectorSet - 'connect-the-dots'
Bio::EBI::RNAseqAPI - A Perl interface to the EMBL-EBI RNA-seq analysis API.
This module provides a Perl-based interface to the EMBL-EBI <http://www.ebi.ac.uk> RNA-seq analysis API <http://www.ebi.ac.uk/fg/rnaseq/api/>. The RNA-seq Analysis API enables access to analysis results for thousands of publicly available gene expres...
MKEAYS/Bio-EBI-RNAseqAPI-1.04 - 09 Sep 2016 15:06:17 UTC - Search in distribution
Bio::fastAPD - rapid calculation of average pairwise difference (APD) for multiple sequence alignments
The Bio::fastAPD module provides a computationally efficient method for the calculation of average pairwise difference (APD), a measure of nucleotide diversity, from multiple sequence alignment (MSA) data. This module also provides rapid standard err...
JDBAUGHER/Bio-fastAPD-1.10.0 - 08 Apr 2015 20:59:21 UTC - Search in distribution
Bio::ToolBox::Data - Reading, writing, and manipulating data structure
This module works with the primary Bio::ToolBox Data structure. Simply, it is a complex data structure representing a tabbed-delimited table (array of arrays), with plenty of options for metadata. Many common bioinformatic file formats are simply tab...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution
Chemistry::File::PDB - Protein Data Bank file format reader/writer
This module reads and writes PDB files. The PDB file format is commonly used to describe proteins, particularly those stored in the Protein Data Bank (<http://www.rcsb.org/pdb/>). The current version of this module only reads the following record typ...
ITUB/Chemistry-File-PDB-0.23 - 10 May 2009 21:58:55 UTC - Search in distribution
Webservice::InterMine - modules for interacting with InterMine datawarehouse webservices
This distribution is the client interface to any implementation of the InterMine Datawarehousing WebService (www.intermine.org). Primarily used for biological genomic databases, the webservice allows the user to easily write and execute structured qu...
INTERMINE/Webservice-InterMine-1.0405 - 12 Dec 2013 23:14:03 UTC - Search in distribution
Crypt::OpenSSL::CA::Inline::C - A bag of XS and Inline::C tricks
This documentation is only useful for people who want to hack *Crypt::OpenSSL::CA*. It is of no interest for people who just want to use the module. This package provides Inline::C goodness to Crypt::OpenSSL::CA during development, plus a few tricks ...
DOMQ/Crypt-OpenSSL-CA-0.91 - 29 Oct 2021 17:53:22 UTC - Search in distribution