Table of Contents - RDoc Documentation

Pages

• LICENSE

Classes/Modules

• Bio
• Bio::DB
• Bio::DB::FastaLengthDB
• Bio::DB::Pileup
• Bio::DB::Vcf
• Bio::Util
• Bio::Util::Gngm
  • Background
  • Example
  • Polymorphisms and statistics
  • SNPs
  • Short INDELS
  • Insertion Size
  • Unmapped Mate Pairs / Paired Ends.
  • Input types
  • Workflow
  • Prerequisites
  • Acknowledgements
  • Using bio-gngm
  • API

Methods

• ::new — Bio::Util::Gngm
• ::new — Bio::DB::FastaLengthDB
• #alternatives — Bio::DB::Vcf
• #calculate_clusters — Bio::Util::Gngm
• #calculate_densities — Bio::Util::Gngm
• #calculate_signal — Bio::Util::Gngm
• #close — Bio::Util::Gngm
• #clusters — Bio::Util::Gngm
• #collect_threads — Bio::Util::Gngm
• #densities — Bio::Util::Gngm
• #discordant_chastity — Bio::DB::Pileup
• #draw_bands — Bio::Util::Gngm
• #draw_hit_count — Bio::Util::Gngm
• #draw_peaks — Bio::Util::Gngm
• #draw_signal — Bio::Util::Gngm
• #draw_threads — Bio::Util::Gngm
• #each — Bio::DB::FastaLengthDB
• #frequency_histogram — Bio::Util::Gngm
• #get_band — Bio::Util::Gngm
• #get_insert_size_frequency — Bio::Util::Gngm
• #get_peaks — Bio::Util::Gngm
• #get_unmapped_mate_frequency — Bio::Util::Gngm
• #gq — Bio::DB::Vcf
• #hit_count — Bio::Util::Gngm
• #is_allowed_substitution? — Bio::Util::Gngm
• #is_indel? — Bio::DB::Vcf
• #is_mnp? — Bio::DB::Vcf
• #is_snp? — Bio::DB::Vcf
• #is_snp? — Bio::DB::Pileup
• #keep_known_variants — Bio::Util::Gngm
• #mq — Bio::DB::Vcf
• #non_ref_allele_count — Bio::DB::Vcf
• #non_ref_allele_freq — Bio::DB::Vcf
• #pass_quality? — Bio::DB::Vcf
• #peaks — Bio::Util::Gngm
• #pl — Bio::DB::Vcf
• #signal — Bio::Util::Gngm
• #snp_positions — Bio::Util::Gngm
• #snp_positions= — Bio::Util::Gngm
• #threads — Bio::Util::Gngm
• #to_s — Bio::DB::Vcf
• #used_depth — Bio::DB::Vcf
• #variant? — Bio::DB::Vcf