Bio::Coordinate - Modules for working with biological coordinates River stage one • 1 direct dependent • 4 total dependents

Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples....

CJFIELDS/Bio-Coordinate-1.007001 - 15 Dec 2016 05:03:14 UTC - Search in distribution

Bio::EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils River stage zero No dependents

This distribution encompasses a low-level API for interacting with (and storing) information from) NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage...

CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC - Search in distribution


Bio::MedChunker - NP chunker for MEDLINE texts River stage zero No dependents

XERN/Bio-MedChunker-0.02 - 03 Jul 2005 13:42:25 UTC - Search in distribution

Bio::Translator - Translate DNA sequences River stage zero No dependents

"Bio::Translator" tries to be a robust translator object featuring translation tables based off the the ones provided by NCBI <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>. Key features include the ability to handle degenerate nucleotides...

KGALINSKY/Bio-Translator-v0.6.1 - 10 Nov 2011 22:05:59 UTC - Search in distribution

Bio::Cellucidate - Perl library for cellucidate.com River stage zero No dependents

Cellucidate is a tool for computation biologists to run simulations. It is based on the Kappa language. The various objects in Cellucidate are arranged into a book metaphor. The basic hierarchy is: Bookshelves `-> Books `-> Agents `-> Rules `-> Model...

BKANEY/Bio-Cellucidate-0.03 - 05 Mar 2010 06:03:15 UTC - Search in distribution

Bio::FastParsers - Classes for parsing bioinformatic programs output River stage one • 7 direct dependents • 8 total dependents

This distribution includes modules for parsing the output files of a selection of sequence comparison programs, including BLAST <https://blast.ncbi.nlm.nih.gov/>, HMMER <http://hmmer.org/>, CD-HIT <https://github.com/weizhongli/cdhit> and UCLUST <htt...

DBAURAIN/Bio-FastParsers-0.201110 - 20 Apr 2020 21:09:15 UTC - Search in distribution

Bio::IlluminaSAV - Parse Illumina SAV files River stage zero No dependents

Easy access to Illumina's SAV file data....

EARONESTY/Bio-IlluminaSAV-1.0.9706 - 16 Sep 2013 18:59:34 UTC - Search in distribution

Bio::PhyloTastic - Perl clients for PhyloTastic River stage zero No dependents

PhyloTastic (<http://phylotastic.org>) is community effort to develop interoperable tools for pruning and annotating phylogenetic megatrees. This package contributes to that effort by providing simple client access to web services that perform steps ...

RVOSA/Bio-PhyloTastic-0.2 - 11 Jun 2012 18:58:40 UTC - Search in distribution

Bio::PhyloNetwork - Module to compute with Phylogenetic Networks River stage zero No dependents

Phylogenetic Networks This is a module to work with phylogenetic networks. Phylogenetic networks have been studied over the last years as a richer model of the evolutionary history of sets of organisms than phylogenetic trees, because they take not o...

CJFIELDS/Bio-PhyloNetwork-1.7.3 - 25 Sep 2018 01:36:59 UTC - Search in distribution

Bio::GenBankParser - Parse::RecDescent parser for a GenBank record River stage zero No dependents

KCLARK/Bio-GenBankParser-0.05 - 23 Jun 2010 17:00:02 UTC - Search in distribution

Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr River stage zero No dependents

Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers the abi...

SMCKAY/Bio-PrimerDesigner-0.07 - 17 Jul 2009 21:21:16 UTC - Search in distribution

Bio::AutomatedAnnotation - Automated annotation of assemblies River stage zero No dependents

VOFFFORD/Bio-AutomatedAnnotation-1.182770 - 04 Oct 2018 13:47:56 UTC - Search in distribution

Bio::AssemblyImprovement - Improve an assembly by scaffolding, contig ordering and gap closing. River stage zero No dependents

AJPAGE/Bio_AssemblyImprovement-1.160490 - 18 Feb 2016 10:10:42 UTC - Search in distribution

Bio::DB::Ace - Database object interface to ACeDB servers River stage zero No dependents

This provides a standard BioPerl database access to Ace, using Lincoln Steins excellent AcePerl module. You need to download and install the aceperl module from http://stein.cshl.org/AcePerl/ before this interface will work. This interface is designe...

CJFIELDS/Bio-DB-Ace-1.7.3 - 25 Sep 2018 00:11:27 UTC - Search in distribution

Bio::DB::Big - Read files using bigWigLib including BigBED and BigWig River stage one • 1 direct dependent • 1 total dependent

AYATES/Bio-DB-Big-v1.0.1 - 16 Oct 2017 14:14:22 UTC - Search in distribution

Bio::DB::GFF - Storage and retrieval of sequence annotation data River stage one • 2 direct dependents • 2 total dependents

Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this mo...

CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC - Search in distribution

Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files River stage one • 1 direct dependent • 1 total dependent

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 River stage one • 2 direct dependents • 2 total dependents

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::DB::EMBL - Database object interface for EMBL entry retrieval River stage one • 1 direct dependent • 9 total dependents

Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI: <http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>. In order to make changes transparent we have host type (currently only ebi) and location (...

CJFIELDS/Bio-DB-EMBL-1.7.4 - 04 Mar 2019 05:02:40 UTC - Search in distribution

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