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06 May 2020 21:51:14 UTC
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Emmanouil "Manolis" Maragkakis, Panagiotis Alexiou <pan.alexiou@gmail.com>
Modules
A Modern Perl Framework for High Throughput Sequencing analysisConnector to database object, with featuresSchema objectDBIC Result class for sequenced readsDBIC Result class for sequenced readsDBIC Result class for sequenced readsObject implementing methods for accessing bed formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)Object representing a record of a bed fileObject implementing methods for accessing fasta formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)Object representing a record of a fasta fileObject implementing methods for accessing fastq formatted filesObject representing a record of a fastq fileObject implementing methods for accessing GFF formatted files (http://www.sanger.ac.uk/resources/software/gff/spec.html)Object representing a record of a gff fileObject implementing methods for accessing SAM formatted filesRole that corresponds to the SAM file CIGAR stringRole that combines SAM CIGAR string with MD:Z tagRole - The MD:Z tag in a SAM fileObject representing a record of a sam fileObject for a data structure which corresponds of a 2D hash whose values are references to arrayExon objectGene objectFactory for creating GenOO::RegionCollection objectsFactory for creating GenOO::GeneCollection object from a Transcript Collection and a hash{transcript_name} = genenameFactory to create GeneCollection from a GTF fileObject that corresponds to a region on a genomeA collection of useful mathematical methodsIntron objectA junction (eg exon-exon) object with featuresModule that offers methods for searching in an array using binary searchRole that represents a region on a reference sequenceRole for a collection of GenOO::Region objectsFactory for creating GenOO::RegionCollection objectsFactory for creating GenOO::RegionCollection object from a BED fileFactory for creating GenOO::RegionCollection object from a database tableFactory for creating a RegionCollection from array of regionsRole for a concrete factory that creates GenOO::RegionCollection objectsFactory for creating GenOO::RegionCollection object from a SAM fileClass for a collection of GenOO::Region objects stored in a database.Object for a collection of GenOO::Region objects, with featuresRole for a region that can be splicedCorresponds to a gene transcriptTranscript part (coding sequence)A functional region within a transcript consisting of spliceable elementsTranscript part (coding sequence)Transcript part (coding sequence)Role for a collection of GenOO::Transcript objectsFactory for creating GenOO::TranscriptCollection objectsFactory to create GenOO::TranscriptCollection object from a GeneCollectionFactory to create TranscriptCollection from a GTF fileOther files
Module Install Instructions
To install GenOO, copy and paste the appropriate command in to your terminal.
cpanm GenOO
perl -MCPAN -e shell install GenOO
For more information on module installation, please visit the detailed CPAN module installation guide.