Author image Emmanouil "Manolis" Maragkakis
and 1 contributors

Modules

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