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Bio-Gonzales-0.083
River stage zero No dependents

Documentation

aln2aln
convert different alignment formats to another alignment format
fasta-grep
grep fasta files
bg_fasplit.pl
split sequences in fasta files by given regular expression
bg_fastat.pl
fasta file statistics
bg_xlsx2tsv
convert xlsx files to tsv format
coords2gff.pl
convert mummer coords files to gff3 format
fadiff
diff fasta files
fafind-eq-seq
find equal sequences
gonz_unmap.pl
unmap or remap identifiers/strings using a given id mapping
m2x
matrix (CSV) data to xlsx format
ppt_profile_cmd.pl
track the cpu and memory usage of a command
show-align2clustalw.pl
convert mummer alignment files to clustalw format
Bio::Gonzales::Project::Functions
organize your computational experiments

Modules

Bio::Gonzales
Speedy functions to manipulate biological data
Bio::Gonzales::Align::IO
Utility functions for aligment stuff
Bio::Gonzales::Align::IO::Stockholm
IO class for the stockholm format
Bio::Gonzales::Assembly::IO
assembly related stuff
Bio::Gonzales::Domain::Identification::HMMER
Identify Protein Domains with HMMER
Bio::Gonzales::Feat
a sequence feature
Bio::Gonzales::Feat::IO::GFF3
read and write gff files
Bio::Gonzales::Graphics::BLAST
make your blast result nice
Bio::Gonzales::IDMapIO
remap ids of 'objects', should be used in IO-classes, like Bio::SeqIO
Bio::Gonzales::Matrix::IO
Library for simple matrix IO
Bio::Gonzales::Phylo::Dendroscope
Color phylogenetic trees in Dendroscope format
Bio::Gonzales::Phylo::Util
utility functions for phylogenetic analysis
Bio::Gonzales::Project::Functions
analysis project utils
Bio::Gonzales::Range::Cluster
cluster sorted ranges iteratively
Bio::Gonzales::Range::GroupedOverlap
cluster overlapping ranges that are in the same group
Bio::Gonzales::Range::Overlap
find overlapping ranges
Bio::Gonzales::Search::IO::BLAST
Bio::Gonzales::Seq
Gonzales Sequence Object
Bio::Gonzales::Seq::Filter
filter sequence data
Bio::Gonzales::Seq::Filter::ProteinCleaner
clean protein sequences
Bio::Gonzales::Seq::IO
fast utility functions for sequence IO
Bio::Gonzales::SummarizedExperiment
represent experimental matrix-like data (assay) with features and sample info
Bio::Gonzales::Util
Utility functions for common tasks
Bio::Gonzales::Util::Cerial
convenience functions for yaml and json IO
Bio::Gonzales::Util::Development
functions handy for general development
Bio::Gonzales::Util::Development::File
Helper functions for all filesystem related tasks
Bio::Gonzales::Util::Development::Module
functions handy for module development
Bio::Gonzales::Util::File
Utility functions for file stuff
Bio::Gonzales::Util::Graphics::Color::Generator
generate distinguishable colors in RGB format
Bio::Gonzales::Util::Log
basic logging for Bio::Gonzales
Bio::Gonzales::Util::Math
Bio::Gonzales::Util::Math::kNN::via::Distances
Calculate kNN clusterings from already calculated distances
Bio::Gonzales::Util::Role::FileIO
File input & ouput interface for parser classes
Bio::Gonzales::Util::Text
text and string functions
Bio::Gonzales::Var::IO::VCF
parse VCF files

Provides

Bio::Gonzales::Align
in lib/Bio/Gonzales/Align.pm
Bio::Gonzales::Align::ConsensePrimer
in lib/Bio/Gonzales/Align/ConsensePrimer.pm
Bio::Gonzales::Align::ConsensePrimer1
in lib/Bio/Gonzales/Align/ConsensePrimer1.pm
Bio::Gonzales::Align::IO::MAF
in lib/Bio/Gonzales/Align/IO/MAF.pm
Bio::Gonzales::Align::Jalview
in lib/Bio/Gonzales/Align/Jalview.pm
Bio::Gonzales::Domain::Group
in lib/Bio/Gonzales/Domain/Group.pm
Bio::Gonzales::Feat::IO
in lib/Bio/Gonzales/Feat/IO.pm
Bio::Gonzales::Feat::IO::BED
in lib/Bio/Gonzales/Feat/IO/BED.pm
Bio::Gonzales::Feat::IO::Base
in lib/Bio/Gonzales/Feat/IO/Base.pm
Bio::Gonzales::Feat::IO::CDhit
in lib/Bio/Gonzales/Feat/IO/CDhit.pm
Bio::Gonzales::Feat::IO::MUM
in lib/Bio/Gonzales/Feat/IO/MUM.pm
Bio::Gonzales::Feat::IO::SWISS
in lib/Bio/Gonzales/Feat/IO/SWISS.pm
Bio::Gonzales::GO::Util
in lib/Bio/Gonzales/GO/Util.pm
Bio::Gonzales::Graphics::Glyph::colorfulBox
in lib/Bio/Gonzales/Graphics/Glyph/colorfulBox.pm
Bio::Gonzales::Matrix::IO::csv
in lib/Bio/Gonzales/Matrix/IO/csv.pm
Bio::Gonzales::Matrix::Util
in lib/Bio/Gonzales/Matrix/Util.pm
Bio::Gonzales::MiniFeat
in lib/Bio/Gonzales/MiniFeat.pm
Bio::Gonzales::Phylo::IO
in lib/Bio/Gonzales/Phylo/IO.pm
Bio::Gonzales::PrimarySeqIX
in lib/Bio/Gonzales/PrimarySeqIX.pm
Bio::Gonzales::Project
in lib/Bio/Gonzales/Project.pm
Bio::Gonzales::Range::Util
in lib/Bio/Gonzales/Range/Util.pm
Bio::Gonzales::Role::BioPerl::Constructor
in lib/Bio/Gonzales/Role/BioPerl/Constructor.pm
Bio::Gonzales::Search::IO::HMMER3
in lib/Bio/Gonzales/Search/IO/HMMER3.pm
Bio::Gonzales::Seq::Filter::DuplicateSeqs
in lib/Bio/Gonzales/Seq/Filter/DuplicateSeqs.pm
Bio::Gonzales::Seq::IO::Fasta
in lib/Bio/Gonzales/Seq/IO/Fasta.pm
Bio::Gonzales::Seq::IO::fastq
in lib/Bio/Gonzales/Seq/IO/fastq.pm
Bio::Gonzales::Seq::LongestTranscript
in lib/Bio/Gonzales/Seq/LongestTranscript.pm
Bio::Gonzales::Seq::Util
in lib/Bio/Gonzales/Seq/Util.pm
Bio::Gonzales::Seq::Validate::fasta
in lib/Bio/Gonzales/Seq/Validate/fasta.pm
Bio::Gonzales::Stat::Util
in lib/Bio/Gonzales/Stat/Util.pm
Bio::Gonzales::String::Util
in lib/Bio/Gonzales/String/Util.pm
Bio::Gonzales::Tools::SeqMask
in lib/Bio/Gonzales/Tools/SeqMask.pm
Bio::Gonzales::Tools::SeqStats
in lib/Bio/Gonzales/Tools/SeqStats.pm
Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER::SeqMarks
in lib/Bio/Gonzales/Domain/Identification/HMMER/SeqMarks.pm
Bio::Gonzales::Util::IO::Compressed
in lib/Bio/Gonzales/Util/IO/Compressed.pm
Bio::Gonzales::Var::Util
in lib/Bio/Gonzales/Var/Util.pm
Bio::Matrix::IO::mcl
in lib/Bio/Gonzales/Matrix/IO/mcl.pm

Other files