Modules
A Modern Perl Framework for High Throughput Sequencing analysis
Connector to database object, with features
Schema object
Draft DBIx::Class result class for a sequencing sample database table
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
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 for creating a TranscriptCollection with transcripts from a GTF file