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#/ Array
#== Meta::Data
#[] Meta::Data
#add Meta::Pool
#add_filename Bio::Ngs::Illumina::Sample
#add_iterator_for Bio::Ngs::Cufflinks::Utils::ClassMethods
#add_option Bio::Command::Wrapper::ClassMethods
#aliases Bio::Command::Wrapper::ClassMethods
#annotated_isoform? Bio::Ngs::Cufflinks::Transcript
#annotated_isoforms Bio::Ngs::Cufflinks::GtfParser
#attributes Bio::Ngs::Cufflinks::Transcript
#average Enumerable
bar_charts Bio::Ngs::Graphics
binary Bio::Ngs::Utils
blast2text Bio::Ngs::Homology
blast_import Bio::Ngs::Homology
#brand_new_isoform? Bio::Ngs::Cufflinks::Transcript
#brand_new_isoforms Bio::Ngs::Cufflinks::GtfParser
bubble_chart Bio::Ngs::Graphics
#buffer Bio::Ngs::Converter::Qseq
build Bio::Ngs::Illumina
build_compare_kb Bio::Ngs::Cufflinks::Compare
#build_idx Bio::Ngs::Cufflinks::GtfParser
#byte_length Bio::Ngs::Cufflinks::Transcript
cat Bio::Ngs::FS
#chr_notation Bio::Ngs::Cufflinks::Transcript
#class_name Bio::Command::Wrapper
#clear Bio::Ngs::Record
#clear Bio::Ngs::Cufflinks::Transcript
compile_source Bio::Ngs::Utils
#count Bio::Ngs::Cufflinks::GtfParser
#coverage_gt Bio::Ngs::Cufflinks::GtfParser
#create_tables Bio::Ngs::Db
#default_options Bio::Command::Wrapper
#delete_option Bio::Command::Wrapper::ClassMethods
down CreateGo
down CreateBlastout
down CreateGoannotation
down CreateGene
down CreateGeneGo
download_and_uncompress Bio::Ngs::Utils
download_with_progress Bio::Ngs::Utils
draw_area Bio::Ngs::Graphics
#dump_idx Bio::Ngs::Cufflinks::GtfParser
#each Meta::Pool
#each_transcript Bio::Ngs::Cufflinks::GtfParser
#empty? Meta::Pool
exists_kb? Bio::Ngs::Cufflinks::Compare
#exons Bio::Ngs::Cufflinks::Transcript
#exons= Bio::Ngs::Cufflinks::Transcript
#export Bio::Ngs::Db
extend_system_path Bio::Ngs::Utils
#feature Bio::Ngs::Cufflinks::Transcript
#filenames_paths Bio::Ngs::Illumina::Sample
files Bio::Ngs::FS
#filter Bio::Ngs::Illumina
find_binary_files Bio::Ngs::Utils
#format Bio::Ngs::FastQuality
#frame Bio::Ngs::Cufflinks::Transcript
#gene_id Bio::Ngs::Ontology
genes Bio::Ngs::Cufflinks::Diff
#get Meta::Pool
#get_by_name Meta::Pool
#get_by_tag Meta::Pool
#get_by_tag_and_value Meta::Pool
#get_by_value Meta::Pool
#get_down_to_childer Meta::Pool
#get_new_transcripts Bio::Ngs::Cufflinks::QuantificationDenovo
#get_transcript Bio::Ngs::Cufflinks::GtfParser
gets_compressed Bio::Ngs::Illumina::FastqGz
gets_filtered Bio::Ngs::Illumina::FastqGz
gets_uncompressed Bio::Ngs::Illumina::FastqGz
#go Bio::Ngs::Ontology
go_annotation_to_json Bio::Ngs::Homology
go_import Bio::Ngs::Ontology
goa_import Bio::Ngs::Homology
#has_tag? Meta::Data
#has_value? Meta::Data
#help Bio::Ngs::Runner
included Bio::Ngs::Cufflinks::Utils
included Bio::Command::Wrapper
#index Bio::Ngs::Cufflinks::GtfParser
#inherited Bio::Command::Wrapper::ClassMethods
#initialize Bio::Ngs::Db
#initialize Bio::Ngs::Cufflinks::Transcript
#initialize Bio::Ngs::Illumina::Project
#initialize Bio::Ngs::Illumina::Projects
#initialize Bio::Command::Wrapper
#initialize Bio::Ngs::Illumina::Sample
#initialize Meta::Pool
#initialize Meta::Data
#initialize Bio::Ngs::Cufflinks::Gtf
#initialize Bio::Ngs::Ontology
#initialize Bio::Ngs::Converter::Qseq
#initialize Bio::Ngs::Record
#initialize Bio::Ngs::FastQuality
#initialize Bio::Ngs::Utils::BinaryNotFound
#initialize Bio::Ngs::Illumina::MetaReads
#insert_many Bio::Ngs::Db
install_binary Bio::Ngs::Utils
#is_lazy? Bio::Ngs::Cufflinks::GtfParser
#is_numeric? String
isoforms Bio::Ngs::Cufflinks::Diff
json_create Meta::Pool
json_create Meta::Data
json_create Bio::Ngs::Illumina::MetaReads
just_make Bio::Ngs::Utils
kb_name Bio::Ngs::Cufflinks::Compare
#lazy Bio::Ngs::Cufflinks::GtfParser
#length_gt Bio::Ngs::Cufflinks::GtfParser
#library Bio::Ngs::Ontology
#load Bio::Ngs::Record
load_compare_kb Bio::Ngs::Cufflinks::Compare
load_go_genes Bio::Ngs::Ontology
#load_idx Bio::Ngs::Cufflinks::GtfParser
#mark Bio::Ngs::Cufflinks::MarkCall
#metadata Meta::Data
#mono_exon Bio::Ngs::Cufflinks::GtfParser
#mono_exon? Bio::Ngs::Cufflinks::Transcript
#multi_exon_with_lengh_and_coverage Bio::Ngs::Cufflinks::GtfParser
#multi_exons Bio::Ngs::Cufflinks::GtfParser
#multi_exons? Bio::Ngs::Cufflinks::Transcript
#name Meta::Data
#name= Meta::Data
#names Meta::Pool
#new_isoform? Bio::Ngs::Cufflinks::Transcript
#new_isoforms Bio::Ngs::Cufflinks::GtfParser
#normalize_params Bio::Command::Wrapper
#not_lazy Bio::Ngs::Cufflinks::GtfParser
offset_by_version Bio::Ngs::Cufflinks::Diff
#options Bio::Command::Wrapper::ClassMethods
#options Bio::Command::Wrapper
#options= Bio::Command::Wrapper
os_type Bio::Ngs::Utils
#output Bio::Command::Wrapper::ClassMethods
#output Bio::Command::Wrapper
#paired? Bio::Ngs::Illumina::Sample
#params Bio::Command::Wrapper
#params= Bio::Command::Wrapper
#path Bio::Ngs::Illumina::Sample
#path Bio::Command::Wrapper
#path Bio::Ngs::Illumina::Project
#path= Bio::Command::Wrapper
#pipe_ahead Bio::Command::Wrapper
#pipe_ahead= Bio::Command::Wrapper
#pipe_ahead? Bio::Command::Wrapper
#pool Meta::Pool
#program Bio::Command::Wrapper::ClassMethods
#program Bio::Command::Wrapper
project_directory? Bio::Ngs::Illumina
#qseq2fastq_pe Bio::Ngs::Converter::Qseq
#qseq2fastq_se Bio::Ngs::Converter::Qseq
#quality_profile Bio::Ngs::FastQuality
#read_transcript Bio::Ngs::Cufflinks::GtfParser
#reset_params Bio::Command::Wrapper
#root_dir Bio::Ngs::Illumina::Project
#run Thor::Task
#run Bio::Command::Wrapper
#sample_sheet Bio::Ngs::Illumina::Project
#sample_variance Enumerable
#samples_path Bio::Ngs::Illumina::Project
#save Bio::Ngs::Record
#save Bio::Ngs::Cufflinks::GtfParser
#score Bio::Ngs::Cufflinks::Transcript
#select Bio::Ngs::Cufflinks::GtfParser
#seqname Bio::Ngs::Cufflinks::Transcript
#set_ensembl_notation Bio::Ngs::Cufflinks::Transcript
#set_lazy Bio::Ngs::Cufflinks::GtfParser
#set_output Bio::Command::Wrapper::ClassMethods
#set_ucsc_notation Bio::Ngs::Cufflinks::Transcript
#size Bio::Ngs::Cufflinks::Transcript
skip_check_binaries Bio::Ngs::Utils
skip_check_binaries? Bio::Ngs::Utils
#skip_task? Bio::Ngs::Utils::BinaryNotFound
#source Bio::Ngs::Cufflinks::Transcript
#source Bio::Ngs::Cufflinks::Gtf
#source= Bio::Ngs::Cufflinks::Gtf
#standard_deviation Enumerable
#start Bio::Ngs::Cufflinks::Transcript
#stats Bio::Ngs::Converter::Qseq
#stop Bio::Ngs::Cufflinks::Transcript
#strand Bio::Ngs::Cufflinks::Transcript
#sub_program Bio::Command::Wrapper::ClassMethods
#sub_program Bio::Command::Wrapper
#sum Enumerable
#symbolize_keys Thor::CoreExt::HashWithIndifferentAccess
tag_filename Bio::Ngs::Utils
#thor_task Bio::Command::Wrapper
#to_bed Bio::Ngs::Cufflinks::GtfParser
#to_bed Bio::Ngs::Cufflinks::Transcript
#to_cmd_ary Bio::Command::Wrapper
#to_db Bio::Ngs::Ontology
#to_db Bio::Ngs::OntologyCollection
#to_fastq Bio::Ngs::Converter::Qseq
#to_gff3 Bio::Ngs::Cufflinks::GtfParser
#to_json Bio::Ngs::Illumina::Project
#to_json Bio::Ngs::Illumina::Sample
#to_json Bio::Ngs::Illumina::MetaReads
#to_json Meta::Pool
#to_json Meta::Data
#to_s Bio::Ngs::Cufflinks::Transcript
#tra Bio::Ngs::Cufflinks::Transcript
#tra= Bio::Ngs::Cufflinks::Transcript
#track_b_count Bio::Ngs::FastQuality
#type Bio::Ngs::Converter::Qseq
uncompress_any Bio::Ngs::Utils
uncompress_command Bio::Ngs::Utils
uncompress_gz_file Bio::Ngs::Utils
up CreateGeneGo
up CreateBlastout
up CreateGene
up CreateGo
up CreateGoannotation
#use_aliases Bio::Command::Wrapper::ClassMethods
#use_aliases? Bio::Command::Wrapper
version Bio::Ngs::Cufflinks::Diff
version Bio::Ngs::Cufflinks