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GenOO-1.5.2
River stage one • 3 direct dependents • 3 total dependents
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  • 06 May 2020 21:51:14 UTC
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Author image Emmanouil "Manolis" Maragkakis
and 1 contributors

Modules

GenOO
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO::Data::DB::Connector
Connector to database object, with features
GenOO::Data::DB::DBIC::Species::Schema
Schema object
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v1
DBIC Result class for sequenced reads
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v2
DBIC Result class for sequenced reads
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3
DBIC Result class for sequenced reads
GenOO::Data::File::BED
Object implementing methods for accessing bed formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)
GenOO::Data::File::BED::Record
Object representing a record of a bed file
GenOO::Data::File::FASTA
Object implementing methods for accessing fasta formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)
GenOO::Data::File::FASTA::Record
Object representing a record of a fasta file
GenOO::Data::File::FASTQ
Object implementing methods for accessing fastq formatted files
GenOO::Data::File::FASTQ::Record
Object representing a record of a fastq file
GenOO::Data::File::GFF
Object implementing methods for accessing GFF formatted files (http://www.sanger.ac.uk/resources/software/gff/spec.html)
GenOO::Data::File::GFF::Record
Object representing a record of a gff file
GenOO::Data::File::SAM
Object implementing methods for accessing SAM formatted files
GenOO::Data::File::SAM::Cigar
Role that corresponds to the SAM file CIGAR string
GenOO::Data::File::SAM::CigarAndMDZ
Role that combines SAM CIGAR string with MD:Z tag
GenOO::Data::File::SAM::MDZ
Role - The MD:Z tag in a SAM file
GenOO::Data::File::SAM::Record
Object representing a record of a sam file
GenOO::Data::Structure::DoubleHashArray
Object for a data structure which corresponds of a 2D hash whose values are references to array
GenOO::Exon
Exon object
GenOO::Gene
Gene object
GenOO::GeneCollection::Factory
Factory for creating GenOO::RegionCollection objects
GenOO::GeneCollection::Factory::FromTranscriptCollection
Factory for creating GenOO::GeneCollection object from a Transcript Collection and a hash{transcript_name} = genename
GenOO::GeneCollection::Factory::GTF
Factory to create GeneCollection from a GTF file
GenOO::GenomicRegion
Object that corresponds to a region on a genome
GenOO::Helper::MyMath
A collection of useful mathematical methods
GenOO::Intron
Intron object
GenOO::Junction
A junction (eg exon-exon) object with features
GenOO::Module::Search::Binary
Module that offers methods for searching in an array using binary search
GenOO::Region
Role that represents a region on a reference sequence
GenOO::RegionCollection
Role for a collection of GenOO::Region objects
GenOO::RegionCollection::Factory
Factory for creating GenOO::RegionCollection objects
GenOO::RegionCollection::Factory::BED
Factory for creating GenOO::RegionCollection object from a BED file
GenOO::RegionCollection::Factory::DBIC
Factory for creating GenOO::RegionCollection object from a database table
GenOO::RegionCollection::Factory::RegionArray
Factory for creating a RegionCollection from array of regions
GenOO::RegionCollection::Factory::Requires
Role for a concrete factory that creates GenOO::RegionCollection objects
GenOO::RegionCollection::Factory::SAM
Factory for creating GenOO::RegionCollection object from a SAM file
GenOO::RegionCollection::Type::DBIC
Class for a collection of GenOO::Region objects stored in a database.
GenOO::RegionCollection::Type::DoubleHashArray
Object for a collection of GenOO::Region objects, with features
GenOO::Spliceable
Role for a region that can be spliced
GenOO::Transcript
Corresponds to a gene transcript
GenOO::Transcript::CDS
Transcript part (coding sequence)
GenOO::Transcript::Part
A functional region within a transcript consisting of spliceable elements
GenOO::Transcript::UTR3
Transcript part (coding sequence)
GenOO::Transcript::UTR5
Transcript part (coding sequence)
GenOO::TranscriptCollection
Role for a collection of GenOO::Transcript objects
GenOO::TranscriptCollection::Factory
Factory for creating GenOO::TranscriptCollection objects
GenOO::TranscriptCollection::Factory::FromGeneCollection
Factory to create GenOO::TranscriptCollection object from a GeneCollection
GenOO::TranscriptCollection::Factory::GTF
Factory to create TranscriptCollection from a GTF file

Other files