k3ylabs/cosoco-image-dataset huggingface dataset:
Package: libbiniou-ocaml (1.2.1-1build3)
Section: universe/ocaml
Homepage: https://github.com/ocaml-community/biniou
Depends: libeasy-format-ocaml-sajs5, ocaml-base-4.13.1
Description:  flexible binary data format in OCaml - plugins Biniou is a binary data format designed for speed, safety, ease of use and backward compatibility as protocols evolve. Biniou is vastly equivalent to JSON in terms of functionality but allows implementations about 4 times as fast (see godi-yojson for comparison), with 25-35% space savings. Biniou data can be decoded into human-readable form without knowledge of type definitions except for field and variant names which are represented by 31-bit hashes. . This package contains the shared runtime libraries.
Package: libbinutils-dbg (2.38-4ubuntu2.5)
Section: debug
Homepage: https://www.gnu.org/software/binutils/
Depends: libbinutils (= 2.38-4ubuntu2.5)
Description:  GNU binary utilities (private shared library, debug symbols) This package provides debug symbols for libbinutils.
Package: libbinutils (2.38-4ubuntu2.5)
Section: devel
Homepage: https://www.gnu.org/software/binutils/
Depends: libc6 (>= 2.34), zlib1g (>= 1:1.2.0), binutils-common (= 2.38-4ubuntu2.5)
Description:  GNU binary utilities (private shared library) This package includes the private shared libraries libbfd and libopcodes.
Package: libbio-alignio-stockholm-perl (1.7.3-2)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-AlignIO-stockholm
Depends: perl:any, libbio-perl-perl
Description:  stockholm sequence input/output stream Indexes Stockholm format alignments such as those from Pfam and Rfam. Returns raw stream data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO). . Bio::AlignIO::stockholm also allows for ID parsing using a callback:
Package: libbio-asn1-entrezgene-perl (1.730-2)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-ASN1-EntrezGene
Depends: perl:any, libbio-cluster-perl, libbio-perl-perl
Description:  parser for NCBI Entrez Gene and NCBI Sequence records Bio::ASN1::EntrezGene and Bio::ASN1::Sequence are regular expression-based parsers for NCBI Entrez Gene genome databases (<http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene>). . They parse ASN.1-formatted Entrez Gene records and NCBI sequences, returning data structures that contain all data items from the gene records or the sequence records. . The parser will report error & line number if input data does not conform to the NCBI Entrez Gene genome or NCBI Sequence annotation file format. . Bio::ASN1::Sequence is basically a modified version of the high-performance Bio::ASN1::EntrezGene parser. However this standalone module exists since it is more efficient to keep Sequence-specific code out of EntrezGene.pm.
Package: libbio-chado-schema-perl (0.20000-3)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-Chado-Schema
Depends: perl:any, libbio-perl-perl, libcarp-clan-perl, libdbix-class-perl, libdbix-class-tree-nestedset-perl
Description:  DBIx::Class layer for the Chado database schema The module Bio::Chado::Schema is a standard object-relational mapping layer for use with the GMOD Chado database schema. Chado is an open-source modular database schema for biological data.
Package: libbio-cluster-perl (1.7.3-5)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-Cluster
Depends: perl:any, libbio-perl-perl, libbio-variation-perl
Description:  BioPerl cluster modules The ClusterIO module works with the ClusterIO format module to read various cluster formats such as NCBI UniGene.
Package: libbio-coordinate-perl (1.7.1-4)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-Coordinate
Depends: perl:any, bioperl (>= 1.7.1)
Description:  BioPerl modules for working with biological coordinates The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. . Since BioPerl version 1.7 several modules where split into separate projects. This package provides the Bio::Coordinate module for working with biological coordinates.
Package: libbio-das-lite-perl (2.11-8)
Section: universe/perl
Homepage: http://biodas.org/
Depends: perl:any, libio-stringy-perl, libreadonly-perl, libwww-curl-perl, libwww-perl
Description:  implementation of the BioDas protocol Bio::Das::Lite is an implementation of the BioDas protocol for the retrieval of biological data from XML sources over HTTP. . Bio::Das::Lite is designed as a lightweight and more forgiving alternative to the client/retrieval/parsing components of Bio::Das. Bio::Das::Lite itself is not a drop-in replacement for Bio::Das but it can be subclassed to do so.
Package: libbio-db-ace-perl (1.7.3-2)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-Ace
Depends: perl, libace-perl, libbio-perl-perl, libbio-db-gff-perl
Description:  Database object interface to ACeDB servers This provides a standard BioPerl database access to Ace, using Lincoln Steins excellent AcePerl module. . This interface is designed at the moment to work through a aceclient/aceserver type mechanism
Package: libbio-db-biofetch-perl (1.7.3-4)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-BioFetch
Depends: perl:any, libbio-perl-perl, libhttp-message-perl, libwww-perl
Description:  Database object interface to BioFetch retrieval Bio::DB::BioFetch is a guaranteed best effort sequence entry fetching method. It goes to the Web-based dbfetch server located at the EBI (http://www.ebi.ac.uk/Tools/dbfetch/dbfetch) to retrieve sequences in the EMBL or GenBank sequence repositories. . Bio::DB::BioFetch implements all the Bio::DB::RandomAccessI interface, plus the get_Stream_by_id() and get_Stream_by_acc() methods that are found in the Bio::DB::SwissProt interface.
Package: libbio-db-embl-perl (1.7.4-4)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-EMBL
Depends: perl:any, libbio-perl-perl, libhttp-message-perl, libwww-perl
Description:  Database object interface for EMBL entry retrieval Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. . In order to make changes transparent host type (currently only ebi) and location (defaults to ebi) were separated out. This allows later additions of more servers in different geographical locations. . The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI.
Package: libbio-db-gff-perl (1.7.4-1)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-GFF
Depends: perl:any, libapache-dbi-perl, libbio-perl-perl, libbio-db-biofetch-perl, libcgi-pm-perl
Description:  Storage and retrieval of sequence annotation data Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. . The following operations are supported by this module: .  - retrieving a segment of sequence based on the ID of a landmark .  - retrieving the DNA from that segment .  - finding all annotations that overlap with the segment .  - finding all annotations that are completely contained within the segment .  - retrieving all annotations of a particular type, either within a segment, or globally .  - conversion from absolute to relative coordinates and back again, using any arbitrary landmark for the relative coordinates .  - using a sequence segment to create new segments based on relative offsets
Package: libbio-db-hts-perl (3.01-3build2)
Section: universe/science
Homepage: https://metacpan.org/release/Bio-DB-HTS
Depends: perl, perlapi-5.34.0, libc6 (>= 2.34), libhts3 (>= 1.10), zlib1g (>= 1:1.2.3.3), libbio-perl-perl
Description:  Perl interface to the HTS library HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension 'csi' (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package provides a Perl interface to the HTS library.
Package: libbio-db-ncbihelper-perl (1.7.7-1)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-NCBIHelper
Depends: perl:any, libbio-perl-perl, libbio-asn1-entrezgene-perl (>> 1.730), libcache-cache-perl, libcgi-pm-perl, libhttp-message-perl, liburi-perl, libwww-perl, libxml-twig-perl
Description:  collection of routines useful for queries to NCBI databases Provides a single place to setup some common methods for querying NCBI web databases. Bio::DB::NCBIHelper just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in postprocess_data(). . The base NCBI query URL used is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
Package: libbio-db-refseq-perl (1.7.4-1)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-RefSeq
Depends: perl, libhttp-message-perl, libwww-perl, libbio-perl-perl
Description:  Database object interface for RefSeq retrieval Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq nucleotide database using the dbfetch script at EBI: . http://www.ebi.ac.uk/Tools/dbfetch/dbfetch . At this time the module specifically retrieves nucleotide sequences only. . In order to make changes transparent host type (currently only ebi) and location (defaults to ebi) were separated out. This allows later additions of more servers in different geographical locations. . The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI.
Package: libbio-db-seqfeature-perl (1.7.4-1)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-SeqFeature
Depends: perl:any, libbio-perl-perl, libbio-db-gff-perl, libdbd-pg-perl, libdbd-sqlite3-perl, libdbi-perl
Description:  Normalized feature for use with Bio::DB::SeqFeature::Store The Bio::DB::SeqFeature object is the default SeqFeature class stored in Bio::DB::SeqFeature databases. It implements both the Bio::DB::SeqFeature::NormalizedFeatureI and Bio::DB::SeqFeature::NormalizedTableFeatureI interfaces, which means that its subfeatures, if any, are stored in the database in a normalized fashion, and that the parent/child hierarchy of features and subfeatures are also stored in the database as set of tuples. This provides efficiencies in both storage and retrieval speed. . Typically you will not create Bio::DB::SeqFeature directly, but will ask the database to do so on your behalf, as described in Bio::DB::SeqFeature::Store.
Package: libbio-db-swissprot-perl (1.7.4-1)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-DB-SwissProt
Depends: perl, libbio-perl-perl, libhttp-message-perl, libwww-perl
Description:  Database object interface to SwissProt retrieval SwissProt is a curated database of proteins managed by the Swiss Bioinformatics Institute. Additional tools for parsing and manipulating swissprot files can be found at ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/. . Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the SwissProt database via an Expasy retrieval. . In order to make changes transparent host type (currently only expasy) and location (default to Switzerland) is separated out. This allows the user to pick the closest Expasy mirror for running their queries.
Package: libbio-eutilities-perl (1.77-1)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-EUtilities
Depends: perl:any, libbio-asn1-entrezgene-perl, libbio-perl-perl, libhttp-message-perl, libtext-csv-perl, liburi-perl, libwww-perl, libxml-simple-perl
Description:  BioPerl interface to the Entrez Programming Utilities (E-utilities) The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules.  This package provides a programmatic interface to NCBI's Entrez Programming Utilities commonly referred to as E-utilities.  Namely, it provides the Bio::DB::EUtilities and Bio::Tools::EUtilities perl modules. . Entrez is a federated search engine at the National Center for Biotechnology Information (NCBI) for a large number of databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature.  E-utilities are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI).
Package: libbio-featureio-perl (1.6.905-2)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-FeatureIO
Depends: perl:any, libbio-perl-perl, libscalar-list-utils-perl, libtree-dagnode-perl, liburi-perl, libxml-dom-perl, libxml-dom-xpath-perl
Description:  Modules for reading, writing, and manipulating sequence features An I/O iterator subsystem for genomic sequence features. . Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should use. . The Bio::FeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI. . The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object.
Package: libbio-graphics-perl (2.40-6)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-Graphics
Depends: perl, bioperl, libgd-gd2-perl, libbio-db-seqfeature-perl
Description:  Generate GD images of Bio::Seq objects The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature, Das::Segment::Feature and Bio::DB::Graphics objects.  It can be used to draw sequence annotations, physical (contig) maps, protein domains, or any other type of map in which a set of discrete ranges need to be laid out on the number line.
Package: libbio-mage-perl (20030502.3-6)
Section: universe/perl
Homepage: http://mged.sourceforge.net/
Depends: perl:any, libtie-ixhash-perl
Description:  Container module for classes in the MAGE package: MAGE MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the Microarray Gene Expression Data Society (MGED). This package contains Perl modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum Information About a Microarray Experiment) records of microarray ("DNA chips") experiments. . The Bio::MAGE module contains the following Bio::MAGE classes:  * NameValueType  * Extendable  * Identifiable  * Describable
Package: libbio-mage-utils-perl (20030502.0-5)
Section: universe/perl
Homepage: http://mged.sourceforge.net/
Depends: perl:any, libtie-ixhash-perl
Description:  Extra modules for classes in the MAGE package: MAGE MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the Microarray Gene Expression Data Society (MGED). This package contains Perl modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum Information About a Microarray Experiment) records of microarray ("DNA chips") experiments. . Bio-MAGE-Utils contains extra modules for handling MAGE XML and MGED ontology, as well as SQL utilities.
Package: libbio-perl-perl (1.7.8-1)
Section: universe/perl
Homepage: http://www.bioperl.org/
Depends: libio-string-perl, libdata-stag-perl, perl:any
Description:  BioPerl core perl modules BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in libbio-perl-perl consist of the core of the functionality of bioperl.
Package: libbio-perl-run-perl (1.7.3-8)
Section: universe/perl
Homepage: https://metacpan.org/release/BioPerl-Run
Depends: perl:any, libbio-perl-perl, libipc-run-perl, libfile-sort-perl
Description:  BioPerl wrappers: modules Contains modules that provide a Perl interface to various bioinformatics applications to allow them to be used with common BioPerl objects.
Package: libbio-primerdesigner-perl (0.07-8)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-PrimerDesigner
Depends: perl:any, libwww-perl, libclass-base-perl, libreadonly-perl, primer3, ncbi-epcr
Description:  Perl module to design PCR primers using primer3 and epcr Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. In addition to accessing local installations of primer3 or e-PCR, it also offers the ability to accessing the primer3 binary via a remote server.
Package: libbio-procedural-perl (1.7.4-2)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-Procedural
Depends: perl:any, libbio-perl-perl
Description:  Simple low-dependency procedural interfaces to BioPerl The code in this distribution focuses on simple low-dependency procedural interfaces to BioPerl that don't require knowledge of BioPerl classes and methods.
Package: libbio-samtools-perl (1.43-3build2.1)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-SamTools
Depends: perl, perlapi-5.34.0, libc6 (>= 2.34), zlib1g (>= 1:1.2.3.3), libbio-perl-perl
Description:  Perl interface to SamTools library for DNA sequencing Bio::SamTools provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application.
Package: libbio-scf-perl (1.03-5build2)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-SCF
Depends: perl, perlapi-5.34.0, libc6 (>= 2.34), libstaden-read14 (>= 1.14.12)
Description:  Perl extension for reading and writing SCF sequence files The Bio::SCF (Standard Chromatogram Format) module allows you to read and update (in a restricted way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back.
Package: libbio-searchio-hmmer-perl (1.7.3-2)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-SearchIO-hmmer
Depends: perl, libbio-perl-perl, libio-string-perl
Description:  perl parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) This object implements a parser for hmmpfam hsp output, a program in the HMMER package. . It is part of the libbio-perl collection.
Package: libbio-tools-phylo-paml-perl (1.7.3-3)
Section: universe/science
Homepage: https://metacpan.org/release/Bio-Tools-Phylo-PAML
Depends: perl:any, libbio-perl-perl, libbio-perl-run-perl, libio-string-perl, paml
Description:  Bioperl interface to the PAML suite This distribution provides a Perl interface to PAML, a suite of programs (baseml, codeml, evolver, and yn00) for phylogenetic analyses of DNA or protein sequences using maximum likelihood. . The Bio::Tools::Run::Phylo::PAML::* modules provide an interface to run the PAML programs while Bio::Tools::Phylo::PAML provides an interface to parse their output files. . This distribution is part of the Bioperl project.
Package: libbio-tools-run-alignment-clustalw-perl (1.7.4-2)
Section: universe/science
Homepage: https://metacpan.org/release/Bio-Tools-Run-Alignment-Clustalw
Depends: perl:any, clustalw, libbio-perl-perl, libbio-perl-run-perl
Description:  Bioperl interface to Clustal W Bio::Tools::Run::Alignment::Clustalw provides a Perl interface to Clustal W, a program for alignment of multiple nucleotide and peptide sequences. . This module distribution is part of the Bioperl project.
Package: libbio-tools-run-alignment-tcoffee-perl (1.7.4-2)
Section: universe/science
Homepage: https://metacpan.org/release/Bio-Tools-Run-Alignment-TCoffee
Depends: perl:any, libbio-perl-perl, libbio-perl-run-perl, t-coffee
Description:  Bioperl interface to T-Coffee Bio::Tools::Run::Alignment::TCoffee provides a Perl interface to T-Coffee, a program for multiple alignments of DNA, RNA, and protein sequences and structures. . This module distribution is part of the Bioperl project.
Package: libbio-tools-run-remoteblast-perl (1.7.3-3)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-Tools-Run-RemoteBlast
Depends: perl:any, libbio-perl-perl, libhttp-message-perl, libio-string-perl, libwww-perl
Description:  Object for remote execution of the NCBI Blast via HTTP Class for remote execution of the NCBI Blast via HTTP. . For a description of the many CGI parameters see: https://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html . Various additional options and input formats are available.
Package: libbio-variation-perl (1.7.5-3)
Section: universe/perl
Homepage: https://metacpan.org/release/Bio-Variation
Depends: perl:any, libbio-perl-perl, libio-string-perl, libxml-twig-perl, libxml-writer-perl
Description:  BioPerl variation-related functionality The code in this distribution focuses on simple low-dependency variant-related functionality for BioPerl. . Bio::Variation name space contains modules to store sequence variation information as differences between the reference sequence and changes sequences. Also included are classes to write out and recrete objects from EMBL-like flat files and XML. Lastly, there are simple classes to calculate values for sequence change objects.
Package: libbiococoa-dev (2.2.2-5build1)
Section: universe/libdevel
Homepage: http://bioinformatics.org/biococoa/
Depends: libbiococoa2 (= 2.2.2-5build1), libgnustep-base-dev
Description:  Bioinformatics framework for GNUstep and Cocoa (development files) BioCocoa is an open source Cocoa framework for bioinformatics. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications. . This package contains the development files, documentation and examples for developing GNUstep applications using the BioCocoa framework.