Bio::CUA - Codon Usage Analyzer. River stage zero No dependents

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::Das - Interface to Distributed Annotation System River stage zero No dependents

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::HTS - XS module providing an interface to htslib River stage zero No dependents

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::SCF - Perl extension for reading and writting SCF sequence files River stage zero No dependents

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 River stage zero No dependents

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::Seq - Sequence object, with features River stage two • 74 direct dependents • 79 total dependents

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-1.7.7 - 07 Dec 2019 19:47:42 UTC - Search in distribution

Bio::ORA - Olfactory Receptor family Assigner (ORA) [bioperl module] River stage zero No dependents

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 River stage zero No dependents

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::Grep - Perl extension for searching in DNA and Protein sequences River stage zero No dependents

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::KEGG - Perl module to fetch details parsed by Bio::KEGGI. River stage zero No dependents

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::Kmer - Helper module for Kmer Analysis. River stage one • 1 direct dependent • 1 total dependent

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-0.41 - 30 Aug 2020 16:32:34 UTC - Search in distribution

Bio::Lite - Lightweight and fast module with a simplified API to ease scripting in bioinformatics River stage zero No dependents

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 River stage zero No dependents

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::Maxd - Perl extension for storing and retrieving data from maxd River stage zero No dependents

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 River stage one • 7 direct dependents • 8 total dependents

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::SDRS - Perl extension for Sigmoidal Dose Response Search, a tool for characterizing biological responses to compounds. River stage zero No dependents

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. River stage zero No dependents

"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 River stage zero No dependents

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::Cigar - Parse CIGAR strings and translate coordinates to/from reference/query River stage zero No dependents

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-1.01 - 05 Jan 2015 18:13:09 UTC - Search in distribution

Bio::ECell - Perl interface for E-Cell Simulation Environment. River stage zero No dependents

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

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