Bio::SeqIO::excel - sequence input/output stream from a MSExcel-formatted table River stage zero No dependents

This class transforms records in a MS Excel workbook file into Bio::Seq objects. It is derived from the table format module and merely defines additional properties and overrides the way to get data from the file and advance to the next record. The m...

CJFIELDS/Bio-SeqIO-excel-1.7.3 - 25 Sep 2018 01:30:22 UTC - Search in distribution

Bio::Sketch::Mash River stage one • 1 direct dependent • 1 total dependent

This is a module to read mash files produced by the Mash executable. For more information on Mash, see mash.readthedocs.org. This module is capable of reading mash files. Future versions will read/write mash files....

LSKATZ/Bio-Sketch-Mash-0.9 - 18 Mar 2019 18:22:34 UTC - Search in distribution

Bio::AGP::LowLevel - functions for dealing with AGP files River stage zero No dependents

functions for working with AGP files....

SHEENAMS/Bio-AGP-LowLevel-0.02 - 17 May 2011 18:50:35 UTC - Search in distribution

Bio::Align::Subset - A BioPerl module to generate new alignments as subset from larger alignments River stage zero No dependents

Given an array of codon positions and an alignment, the function Bio::Align::Subset->build_subset returns a new alignment with the codons at those positions from the original alignment....

HVALVERDE/Bio-Align-Subset-1.27 - 08 May 2013 17:33:42 UTC - Search in distribution

Bio::Chado::Schema - A standard DBIx::Class layer for the Chado database schema. River stage one • 3 direct dependents • 3 total dependents

This is a standard object-relational mapping layer for use with the GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of the very fine DBIx::Class::Schema::Loader module. Chado is an open-source modular d...

RBUELS/Bio-Chado-Schema-0.20000 - 06 Jul 2012 19:06:31 UTC - Search in distribution

Bio::DB::SwissProt - Database object interface to SwissProt retrieval River stage one • 1 direct dependent • 9 total dependents

SwissProt is a curated database of proteins managed by the Swiss Bioinformatics Institute. Additional tools for parsing and manipulating swissprot files can be found at ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/. Allows the dynamic retrie...

CJFIELDS/Bio-DB-SwissProt-1.7.4 - 07 Dec 2019 22:09:00 UTC - Search in distribution

Bio::MUST::Drivers - Bio::MUST classes for driving external programs River stage one • 4 direct dependents • 4 total dependents

External dependencies are installed automatically at first use if the "brew" executable is available in the $PATH. Alternatively, dependencies can be installed (either using "apt-get", "brew" or manually) by the user prior or after installing the dis...

DBAURAIN/Bio-MUST-Drivers-0.193030 - 30 Oct 2019 20:35:27 UTC - Search in distribution

Bio::NEXUS::Import - Extends Bio::NEXUS with parsers for file formats of popular phylogeny programs River stage zero No dependents

A module that extends Bio::NEXUS with parsers for file formats of popular phylogeny programs....

LIMAONE/Bio-NEXUS-Import-v0.2.0 - 03 Feb 2011 16:30:11 UTC - Search in distribution

Bio::Phylo::Beagle - Perl wrapper around BEAGLE River stage zero No dependents

This is a wrapper around the Beagle library (<http://dx.doi.org/10.1093/sysbio/syr100>) that accepts Bio::Phylo objects to simplify data handling....

RVOSA/Bio-Phylo-Beagle-0.03 - 04 Mar 2012 12:39:35 UTC - Search in distribution

Bio::Phylo::CIPRES - Reusable components for CIPRES REST API access River stage zero No dependents

The CyberInfrastructure for Phylogenetic RESearch (CIPRES <http://www.phylo.org>) is a portal that provides access to phylogenetic analyses tools that can be run on the XSEDE HPC infrastructure. The portal has a web browser (point and click) interfac...

RVOSA/Bio-Phylo-CIPRES-v0.2.1 - 17 Apr 2020 22:55:30 UTC - Search in distribution
  • cipresrun - command line interface to the CIPRES analysis portal

Bio::Tools::DNAGen - Generating a pool of DNA sequences River stage zero No dependents

This module is a tool for generating a pool of DNA sequences which meet some logical and physical requirements such as uniqueness, melting temperature and GC ratio. When you have set the parameters, this module will create an array of sequences for y...

XERN/Bio-Tools-DNAGen-0.02 - 06 Apr 2003 09:26:56 UTC - Search in distribution

Bio::Variation::IO - Handler for sequence variation IO Formats River stage two • 1 direct dependent • 15 total dependents

Bio::Variation::IO is a handler module for the formats in the Variation IO set (eg, Bio::Variation::IO::flat). It is the officially sanctioned way of getting at the format objects, which most people should use. The structure, conventions and most of ...

CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC - Search in distribution

Bio::ASN1::Sequence - Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences. River stage two • 2 direct dependents • 13 total dependents

Bio::ASN1::Sequence is a regular expression-based Perl Parser for ASN.1-formatted NCBI sequences. It parses an ASN.1-formatted sequence record and returns a data structure that contains all data items from the sequence record. The parser will report ...

CJFIELDS/Bio-ASN1-EntrezGene-1.73 - 25 Sep 2018 02:32:11 UTC - Search in distribution

Bio::DB::Das::Chado - DAS-style access to a chado database River stage zero No dependents

Bio::DB::Das::Chado allows DAS style access to a Chado database, getting SeqFeatureI-compliant BioPerl objects and allowing GBrowse to access a Chado database directly....

SCAIN/Bio-DB-Das-Chado-0.35a - 07 Apr 2015 23:02:17 UTC - Search in distribution

Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store River stage zero No dependents

The Bio::DB::SeqFeature object is the default SeqFeature class stored in Bio::DB::SeqFeature databases. It implements both the Bio::DB::SeqFeature::NormalizedFeatureI and Bio::DB::SeqFeature::NormalizedTableFeatureI interfaces, which means that its s...

CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution

Bio::Das::ProServer River stage zero No dependents

ProServer is a server implementation of the DAS protocol. http://biodas.org/ ProServer is based on example preforking POEserver at http://poe.perl.org/?POE_Cookbook/Web_Server_With_Forking...

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC - Search in distribution

Bio::EBI::RNAseqAPI - A Perl interface to the EMBL-EBI RNA-seq analysis API. River stage zero No dependents

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::GFF3::LowLevel - fast, low-level functions for parsing and formatting GFF3 River stage one • 1 direct dependent • 1 total dependent

These are low-level, fast functions for parsing GFF version 3 files. All they do is convert back and forth between low-level Perl data structures and GFF3 text. Sometimes this is what you need when you are just doing simple transformations on GFF3. I...

RBUELS/Bio-GFF3-2.0 - 28 Feb 2014 22:01:14 UTC - Search in distribution

Bio::Grid::Run::SGE - Distribute (biological) analyses on the local SGE grid River stage zero No dependents

Control flow in Bio::Grid::Run::SGE The general flow starts at running the cluster script. The script defines an index and an iterator. Indices describe how to split the data into chunks, whereas iterators describe in what order these chunks get fed ...

JWB/Bio-Grid-Run-SGE-0.066 - 20 Nov 2018 22:38:51 UTC - Search in distribution

Bio::LITE::Taxonomy - Lightweight and efficient taxonomic tree manager River stage two • 2 direct dependents • 10 total dependents

This module provides easy and efficient access to different taxonomies (NCBI and RDP) with minimal dependencies and without intermediate databases. This module should be used through specific taxonomic interfaces (e.g. Bio::LITE::Taxonomy::NCBI or Bi...

MOTIF/Bio-LITE-Taxonomy-0.07 - 24 May 2011 11:20:38 UTC - Search in distribution

309 results (0.153 seconds)