Search results for "Bio::*"
Bio::CUA - Codon Usage Analyzer.
The aim of this distribution is to provide comprehensive and flexible tools to analyze codon usage bias (CUB) and relevant problems, so that users can speed up the genetic research by taking advantage of this convenience. One amino acid can be encode...
FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC - Search in distribution- Bio::CUA::Seq - a module processing sequence object
- Bio::CUA::CUB - This is the parent class for all classs processing codon usage bias (CUB).
- Bio::CUA::SeqIO - a package to parse sequence file if module Bio::SeqIO is unavailable in the system.
- 9 more results from Bio-CUA »
Bio::Das - Interface to Distributed Annotation System
Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:...
LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC - Search in distribution- Bio::Das::DSN - Object encapsulation of a DAS data source
- Bio::Das::Map - Resolve map coordinates
- Bio::Das::Util - Das Utilities
- 22 more results from Bio-Das »
Bio::HTS - XS module providing an interface to htslib
The beginnings of an XS wrapper around the many useful methods in htslib. All the other perl modules use the old samtools or aren't on cpan. So far only Tabix is supported. Contributions welcome on github: <http://www.github.com/congenica/perl_htslib...
NYET/Bio-HTS-v0.0.1 - 11 Jan 2016 11:58:54 UTC - Search in distribution- Bio::HTS::VCF - start of an interface to the bcf/vcf utilities in htslib
- Bio::HTS::File - XS module providing an interface to c htsFile structs
- Bio::HTS::Tabix - Object oriented access to the underlying tbx C methods
- 1 more result from Bio-HTS »
Bio::SCF - Perl extension for reading and writting SCF sequence files
This module provides a perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back. Tied Methods $ob...
LDS/Bio-SCF-1.03 - 08 Jan 2010 15:40:35 UTC - Search in distribution
Bio::SFF - Standard Flowgram Format for Perl
This distribution offers various SFF modules. Currently only two readers are provided, in the future a writer will follow....
LEONT/Bio-SFF-0.007 - 25 Jul 2013 14:00:38 UTC - Search in distribution- Bio::SFF::Entry - An SFF entry
- Bio::SFF::Index - SFF index object
- Bio::SFF::Reader - An SFF reader role
- 3 more results from Bio-SFF »
Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::Prim...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::DasI - DAS-style access to a feature database
- Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
- Bio::Range - Pure perl RangeI implementation
- 507 more results from BioPerl »
Bio::ORA - Olfactory Receptor family Assigner (ORA) [bioperl module]
Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 40kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functiona...
CERATITES/ora-2.0 - 14 Jun 2016 15:58:05 UTC - Search in distribution
Bio::GMOD - Unified API for Model Organism Databases
Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN. MODs are highly curated resources of biological data. Although they typically inco...
TWH/Bio-GMOD-0.028 - 07 Jul 2005 18:24:47 UTC - Search in distribution- Bio::GMOD::Query - Execute generic queries for different MODs
- Bio::GMOD::Adaptor - Generic factory for Bio::GMOD::Adaptor::* objects
- Bio::GMOD::Util::Mirror - File and directory mirroring
- 15 more results from Bio-GMOD »
Bio::Grep - Perl extension for searching in DNA and Protein sequences
Bio-Grep is a collection of Perl modules for searching in DNA and Protein sequences. It supports different back-ends, most importantly some (enhanced) suffix array implementations. Currently, there is no suffix array tool that works in all scenarios ...
LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC - Search in distribution- Bio::Grep::Root - Superclass for all Bio::Grep* packages
- Bio::Grep::Cookbook - Bio::Grep Cookbook
- Bio::Grep::Benchmarks - Bio::Grep Benchmarks
- 5 more results from Bio-Grep »
Bio::KEGG - Perl module to fetch details parsed by Bio::KEGGI.
This module is used to fetch details from object created by Bio::KEGGI. Create a new Bio::KEGG object is not supported. For more details for different input files, please refer to documents of L<Bio::KEGG::genome>, L<Bio::KEGG::ko>, L<Bio::KEGG::path...
ZEROLIU/Bio-KEGGI-v0.1.50 - 29 Mar 2011 06:56:26 UTC - Search in distribution- Bio::KEGGI - Perl module to parse KEGG genome, ko and pathway files.
- Bio::KEGG::ko
- Bio::KEGGI::ko
- 4 more results from Bio-KEGGI »
Bio::Kmer - Helper module for Kmer Analysis.
A module for helping with kmer analysis. The basic methods help count kmers and can produce a count of counts. Currently this module only supports fastq format. Although this module can count kmers with pure perl, it is recommended to give the option...
LSKATZ/Bio-Kmer-0.5 - 08 Jan 2024 01:17:10 UTC - Search in distribution
Bio::Lite - Lightweight and fast module with a simplified API to ease scripting in bioinformatics
Bio::Lite is a set of subroutines that aims to answer similar questions as Bio-perl distribution in a FAST and SIMPLE way. Bio::Lite does not make use of complexe data struture, or objects, that would lead to a slow execution. All methods can be impo...
JAUDOUX/Bio-Lite-0.003 - 23 Jul 2014 16:15:45 UTC - Search in distribution
Bio::MAGE - Container module for classes in the MAGE package: MAGE
This is a *package* module that encapsulates a number of classes in the Bio::MAGE hierarchy. These classes belong to the MAGE package of the MAGE-OM object model....
JASONS/Bio-MAGE-20030502.3 - 14 May 2007 10:56:09 UTC - Search in distribution- Bio::MAGE::BQS - Container module for classes in the MAGE package: BQS
- Bio::MAGE::Base - generic base class
- Bio::MAGE::Array - Container module for classes in the MAGE package: Array
- 147 more results from Bio-MAGE »
Bio::Maxd - Perl extension for storing and retrieving data from maxd
Bio::Maxd provides methods for uploading and retrieving data to/from a maxd (MySQL) database. "maxd" is a data warehouse and visualization environment for microarray expression data developed by the Microarray Group at Manchester Bioinformatics (http...
PRILUSKYJ/Bio-Maxd-0.04 - 30 Oct 2002 06:11:03 UTC - Search in distribution
Bio::Perl - Functional access to BioPerl for people who don't know objects
Easy first time access to BioPerl via functions. read_sequence Title : read_sequence Usage : $seq = read_sequence('sequences.fa') $seq = read_sequence($filename,'genbank'); # pipes are fine $seq = read_sequence("my_fetching_program $id |",'fasta'); F...
CJFIELDS/Bio-Procedural-1.7.4 - 29 Nov 2019 20:57:49 UTC - Search in distribution- Bio::Procedural - Simple low-dependency procedural interfaces to BioPerl
Bio::SDRS - Perl extension for Sigmoidal Dose Response Search, a tool for characterizing biological responses to compounds.
Bio::SDRS implements the Sigmoidal Dose Response Search of assay responses described in the paper by Rui-Ru Ji, Nathan O. Siemers, Lei Ming, Liang Schweizer, and Robert E Bruccoleri. The module is implemented using a simple object oriented paradigm w...
BRUC/Bio-SDRS-0.11 - 03 Jan 2015 19:56:37 UTC - Search in distribution
Bio::mGen - a fast and simple gene loading, helping automate BioPerl processes.
"Bio::mGen" This module extracts pre-parsed compressed DNA from "Genbank" and "Refseq" (soon more) databases without draining the NCBI web server resources. Guaranteed to work faster than any module because of the features: Parse-free, compression en...
CYBER/mGen-1.03 - 14 Jan 2006 10:04:36 UTC - Search in distribution
Bio::Chaos - utility class for handling Chaos-XML
This module contains some basic methods for manipulating a Chaos-XML document stored in memory as a Data::Stag tree. This class is fairly minimal. One of the principal ideas being Bio::Chaos is that access to the data model should be directly through...
CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC - Search in distribution- Bio::Chaos::Root - root utility class for chaos objects
- Bio::Chaos::ChaosGraph - object for representing a chaos-xml dataset
- Bio::Chaos::Parser::fasta - fasta sequence input/output stream
- 6 more results from Bio-Chaos »
Bio::Cigar - Parse CIGAR strings and translate coordinates to/from reference/query
Bio::Cigar is a small library to parse CIGAR strings ("Compact Idiosyncratic Gapped Alignment Report"), such as those used in the SAM file format. CIGAR strings are a run-length encoding which minimally describes the alignment of a query sequence to ...
TSIBLEY/Bio-Cigar-1.02 - 28 Oct 2022 23:40:54 UTC - Search in distribution
Bio::ECell - Perl interface for E-Cell Simulation Environment.
Bio::ECell is a Perl interface for the E-Cell Simulation Environment version 3 (http://www.e-cell.org/), a generic cell simulation software for molecular cell biology researches that allow object-oriented modeling and simulation, multi-algorithm/time...
GAOU/Bio-ECell-0.10 - 24 Nov 2009 16:55:50 UTC - Search in distribution