Package: med-bio-dev (3.3)

[ Source: debian-med  ]

Debian Med packages for development of bioinformatics applications

This metapackage will install Debian packages which might be helpful for development of applications for biological research.

Tags: Field: Biology, Role: Metapackage, Application Suite: Debian, Purpose: Need an extra tag

Other Packages Related to med-bio-dev

• dep: med-config (= 3.3)

  Debian Med general config package

• dep: med-tasks (= 3.3)

  Debian Med tasks for tasksel

• rec: bio-tradis

  analyse the output from TraDIS analyses of genomic sequences

• rec: bioperl

  Perl tools for computational molecular biology

• rec: bioperl-run

  BioPerl wrappers: scripts

• rec: biosquid

  utilities for biological sequence analysis

• rec: cwltool

  Common Workflow Language reference implementation

• rec: libace-perl

  Object-Oriented Access to ACEDB Databases

• rec: libai-fann-perl

  Perl wrapper for the FANN library

• rec: libbambamc-dev

  Development files for reading and writing BAM (genome alignment) files

• rec: libbamtools-dev

  C++ API for manipulating BAM (genome alignment) files

• rec: libbio-asn1-entrezgene-perl

  parser for NCBI Entrez Gene and NCBI Sequence records

• rec: libbio-chado-schema-perl

  DBIx::Class layer for the Chado database schema

• rec: libbio-coordinate-perl

  BioPerl modules for working with biological coordinates

• rec: libbio-das-lite-perl

  implementation of the BioDas protocol

• rec: libbio-eutilities-perl

  BioPerl interface to the Entrez Programming Utilities (E-utilities)

• rec: libbio-graphics-perl

  Generate GD images of Bio::Seq objects

• rec: libbio-mage-perl

  Container module for classes in the MAGE package: MAGE

• rec: libbio-mage-utils-perl

  Extra modules for classes in the MAGE package: MAGE

• rec: libbio-primerdesigner-perl

  Perl module to design PCR primers using primer3 and epcr

• rec: libbio-samtools-perl

  Perl interface to SamTools library for DNA sequencing

• rec: libbio-scf-perl

  Perl extension for reading and writing SCF sequence files

• rec: libbio-tools-phylo-paml-perl

  Bioperl interface to the PAML suite

• rec: libbio-tools-run-alignment-clustalw-perl

  Bioperl interface to Clustal W

• rec: libbio-tools-run-alignment-tcoffee-perl

  Bioperl interface to T-Coffee

• rec: libbiococoa-dev

  Bioinformatics framework for GNUstep and Cocoa (development files)

• rec: libbiojava-java

  Java API to biological data and applications (default version)

• rec: libbiojava4-java

  Java API to biological data and applications (default version)
  also a virtual package provided by libbiojava4-java

• rec: libbioparser-dev

  library for parsing several formats in bioinformatics

• rec: libblasr-dev

  tools for aligning PacBio reads to target sequences (development files)

• rec: libbpp-core-dev

  Bio++ Core library development files

• rec: libbpp-phyl-dev

  Bio++ Phylogenetic library development files

• rec: libbpp-phyl-omics-dev

  Bio++ Phylogenetics library: genomics components (development files)

• rec: libbpp-popgen-dev

  Bio++ Population Genetics library development files

• rec: libbpp-qt-dev

  Bio++ Qt Graphic classes library development files

• rec: libbpp-raa-dev

  Bio++ Remote Acnuc Access library development files

• rec: libbpp-seq-dev

  Bio++ Sequence library development files

• rec: libbpp-seq-omics-dev

  Bio++ Sequence library: genomics components (development files)

• rec: libchado-perl

  database schema and tools for genomic data

• rec: libconsensuscore-dev

  algorithms for PacBio multiple sequence consensus -- development files

• rec: libdivsufsort-dev

  libdivsufsort header files

• rec: libedlib-dev

  library for sequence alignment using edit distance (devel)

• rec: libfast5-dev

  library for reading Oxford Nanopore Fast5 files -- headers

• rec: libfastahack-dev

  library for indexing and sequence extraction from FASTA files (devel)

• rec: libffindex0-dev

  library for simple index/database for huge amounts of small files (development)

• rec: libfml-dev

  development headers for libfml

• rec: libfreecontact-dev

  fast protein contact predictor library - development files
  also a virtual package provided by libfreecontact-dev

• rec: libfreecontact-perl

  fast protein contact predictor - binding for Perl

• rec: libgatbcore-dev

  development library of the Genome Analysis Toolbox

• rec: libgenome-dev

  toolkit for developing bioinformatic related software (devel)

• rec: libgenome-model-tools-music-perl

  module for finding mutations of significance in cancer

• rec: libgenome-perl

  pipelines, tools, and data management for genomics

• rec: libgenometools0-dev

  development files for GenomeTools

• rec: libgff-dev

  GFF/GTF parsing from cufflinks as a library

• rec: libgkarrays-dev

  library to query large collection of NGS sequences (development)

• rec: libgo-perl

  perl modules for GO and other OBO ontologies

• rec: libhmsbeagle-dev

  High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)

• rec: libhts-dev

  development files for the HTSlib

• rec: libhtsjdk-java

  Java API for high-throughput sequencing data (HTS) formats

• rec: libjebl2-java

  Java Evolutionary Biology Library

• rec: libjloda-java

  Java library of data structures and algorithms for bioinformatics

• rec: libkmer-dev

  suite of tools for DNA sequence analysis (development lib)

• rec: libmems-dev

  development library to support DNA string matching and comparative genomics

• rec: libminimap-dev

  development headers for libminimap

• rec: libmuscle-dev

  multiple alignment development library for protein sequences

• rec: libncbi-vdb-dev

  libraries for using data in the INSDC Sequence Read Archives (devel)

• rec: libncbi6-dev

  NCBI libraries for biology applications (development files)

• rec: libncl-dev

  NEXUS Class Library (static lib and header files)

• rec: libngs-java

  Next Generation Sequencing language Bindings (Java bindings)

• rec: libngs-sdk-dev

  Next Generation Sequencing language Bindings (development)

• rec: libnhgri-blastall-perl

  Perl extension for running and parsing NCBI's BLAST 2.x

• rec: libopenms-dev

  library for LC/MS data management and analysis - dev files

• rec: libpal-java

  Phylogenetic Analysis Library

• rec: libpbbam-dev

  Pacific Biosciences binary alignment/map (BAM) library (headers)

• rec: libpbdata-dev

  tools for handling PacBio sequences (development files)

• rec: libpbihdf-dev

  tools for handling PacBio hdf5 files (development files)

• rec: libpbseq-dev

  library for analyzing PacBio sequencing data (development files)

• rec: libpll-dev

  Phylogenetic Likelihood Library (development)

• rec: libqes-dev

  DNA sequence parsing library -- development

• rec: librcsb-core-wrapper0-dev

  development files for librcsb-core-wrapper0

• rec: librdp-taxonomy-tree-java

  taxonomy tree library from Ribosomal Database Project (RDP)

• rec: librelion-dev

  C++ API for RELION (3D reconstructions in cryo-electron microscopy)

• rec: librg-blast-parser-perl

  very fast NCBI BLAST parser - binding for Perl

• rec: librg-reprof-bundle-perl

  protein secondary structure and accessibility predictor (perl module)

• rec: librostlab-blast0-dev

  very fast C++ library for parsing the output of NCBI BLAST programs (devel)

• rec: librostlab3-dev

  C++ library for computational biology (development)

• rec: libsbml5-dev

  System Biology Markup Language library - development files

• rec: libseqlib-dev

  C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)

• rec: libsmithwaterman-dev

  determine similar regions between two strings or genomic sequences (devel)

• rec: libsnp-sites1-dev

  Static libraries and header files for the package snp-sites

• rec: libsort-key-top-perl

  Perl module to select and sort top n elements of a list

• rec: libspoa-dev

  SIMD partial order alignment library (development files)

• rec: libsrf-dev

  C++ implementation of the SRF format for DNA sequence data

• rec: libssm-dev

  macromolecular superposition library - development files

• rec: libssw-dev

  Development headers and static libraries for libssw
  also a virtual package provided by libssw-dev

• rec: libssw-java

  Java bindings for libssw

• rec: libstaden-read-dev

  development files for libstaden-read

• rec: libstatgen-dev

  development files for the libStatGen

• rec: libswiss-perl

  Perl API to the UniProt database

• rec: libtabixpp-dev

  C++ wrapper to tabix indexer (development files)
  also a virtual package provided by libtabixpp-dev

• rec: libtfbs-perl

  scanning DNA sequence with a position weight matrix

• rec: libthread-pool-dev

  C++ thread pool library (devel)

• rec: libvcflib-dev

  C++ library for parsing and manipulating VCF files (development)

• rec: libvibrant6-dev

  NCBI libraries for graphic biology applications (development files)

• rec: libzerg-perl

  fast perl module for parsing the output of NCBI BLAST programs

• rec: libzerg0-dev

  development libraries and header files for libzerg

• rec: mcl

  Markov Cluster algorithm

• rec: pyfai

  Fast Azimuthal Integration scripts

• rec: python-biom-format

  Biological Observation Matrix (BIOM) format (Python 2)

• rec: python-cogent

  framework for genomic biology

• rec: python-corepywrap

  library that exports C++ mmCIF accessors to Python

• rec: python-freecontact

  fast protein contact predictor - binding for Python

• rec: python-htseq

  Python high-throughput genome sequencing read analysis utilities
  also a virtual package provided by python3-htseq

• rec: python-kineticstools

  detection of DNA modifications (Python 2 library)

• rec: python-pbcommand

  common command-line interface for Pacific Biosciences analysis modules

• rec: python-pbcore

  Python 2 library for processing PacBio data files

• rec: python-pbh5tools

  tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library

• rec: python-rdkit

  Collection of cheminformatics and machine-learning software

• rec: python3-airr

  Data Representation Standard library for antibody and TCR sequences

• rec: python3-bcbio

  library for analysing high-throughput sequencing data

• rec: python3-biomaj3

  BioMAJ workflow management library

• rec: python3-biopython

  Python library for bioinformatics (implemented in Python 3)

• rec: python3-biotools

  Python3 bioinformatics utilities for high-throughput genomic sequencing

• rec: python3-bx

  library to manage genomic data and its alignment

• rec: python3-cobra

  constraint-based modeling of biological networks with Python 3

• rec: python3-csb

  Python framework for structural bioinformatics (Python3 version)

• rec: python3-cutadapt

  Clean biological sequences from high-throughput sequencing reads (Python 3)

• rec: python3-cyvcf2

  VCF parser based on htslib (Python 3)

• rec: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

• rec: python3-fast5

  library for reading Oxford Nanopore Fast5 files -- Python 3

• rec: python3-gfapy

  flexible and extensible software library for handling sequence graphs

• rec: python3-gffutils

  Work with GFF and GTF files in a flexible database framework

• rec: python3-intervaltree-bio

  Interval tree convenience classes for genomic data -- Python 3 library

• rec: python3-ngs

  Next Generation Sequencing language Bindings (Python3 bindings)

• rec: python3-pbconsensuscore

  algorithms for PacBio multiple sequence consensus -- Python 3

• rec: python3-presto

  toolkit for processing B and T cell sequences

• rec: python3-pybedtools

  Python 3 wrapper around BEDTools for bioinformatics work

• rec: python3-pybel

  Biological Expression Language

• rec: python3-pyfaidx

  efficient random access to fasta subsequences for Python 3

• rec: python3-pymummer

  Python 3 interface to MUMmer

• rec: python3-pysam

  interface for the SAM/BAM sequence alignment and mapping format (Python 3)

• rec: python3-pyvcf

  Variant Call Format (VCF) parser for Python 3

• rec: python3-ruffus

  Python3 computation pipeline library widely used in bioinformatics

• rec: python3-screed

  short nucleotide read sequence utils in Python 3

• rec: python3-sqt

  SeQuencing Tools for biological DNA/RNA high-throughput data

• rec: python3-treetime

  inference of time stamped phylogenies and ancestral reconstruction (Python 3)

• rec: r-bioc-biobase

  base functions for Bioconductor

• rec: r-cran-genetics

  GNU R package for population genetics

• rec: r-cran-haplo.stats

  GNU R package for haplotype analysis

• rec: r-cran-phylobase

  GNU R base package for phylogenetic structures and comparative data

• rec: r-cran-rncl

  GNU R interface to the Nexus Class Library

• rec: r-cran-rnexml

  GNU R package for semantically rich I/O for the 'NeXML' format

• rec: ruby-bio

  Ruby tools for computational molecular biology

• rec: ruby-crb-blast

  Run conditional reciprocal best blast

• rec: sbmltoolbox

  libsbml toolbox for octave and matlab

• rec: seqan-dev

  C++ library for the analysis of biological sequences (development)

• rec: snakemake

  pythonic workflow management system

• rec: toil

  cross-platform workflow engine

• sug: bioclipse

  Package not available

• sug: ctdconverter

  Convert CTD files into Galaxy tool and CWL CommandLineTool files

• sug: galaxy-lib

  Package not available

• sug: libbam-dev

  manipulates nucleotide sequence alignments in BAM or SAM format

• sug: libbigwig-dev

  Package not available

• sug: libbiod-dev

  Package not available

• sug: libdisorder-dev

  library for entropy measurement of byte streams (devel)

• sug: libforester-java

  Package not available

• sug: libfreecontact-doc

  documentation for libfreecontact

• sug: libgoby-java

  Package not available

• sug: libgtextutils-dev

  Gordon Text_utils library (development files)

• sug: libmilib-java

  library for Next Generation Sequencing (NGS) data processing

• sug: libmodhmm-dev

  library for constructing, training and scoring hidden Markov models (dev)

• sug: libnexml-java

  Package not available

• sug: libpbcopper-dev

  data structures, algorithms, and utilities for C++ applications -- header files

• sug: libqcpp-dev

  Package not available

• sug: libroadrunner-dev

  Package not available

• sug: librostlab-blast-doc

  very fast C++ library for parsing the output of NCBI BLAST programs (doc)

• sug: librostlab-doc

  C++ library for computational biology (documentation)

• sug: libsvmloc-dev

  PSORTb adapted library for svm machine-learning library (dev)

• sug: libswarm2-dev

  Package not available

• sug: mgltools-networkeditor

  Python GUI library for the editing of networks

• sug: mgltools-pybabel

  molecular structure file access and interpretation

• sug: mgltools-vision

  Python-based Visual Programming Environment

• sug: octace-bioinfo

  Package not available

• sug: python-biopython-doc

  Documentation for the Biopython library

• sug: python-mmtk

  Package not available

• sug: python-pyflow

  lightweight parallel task engine for Python

• sug: python-roadrunner

  Package not available

• sug: python-screed

  Package not available

• sug: python3-biopython-sql

  Biopython support for the BioSQL database schema (Python 3)

• sug: python3-cgecore

  Package not available

• sug: python3-consensuscore2

  Package not available

• sug: python3-ctdopts

  Gives your Python tools a CTD-compatible interface

• sug: python3-ete3

  Package not available

• sug: python3-hyphy

  Package not available

• sug: python3-mirtop

  Package not available

• sug: python3-misopy

  Package not available

• sug: python3-seqcluster

  Package not available

• sug: python3-skbio

  Package not available

• sug: r-bioc-affy

  BioConductor methods for Affymetrix Oligonucleotide Arrays

• sug: r-bioc-affyio

  BioConductor tools for parsing Affymetrix data files

• sug: r-bioc-altcdfenvs

  BioConductor alternative CDF environments

• sug: r-bioc-annotationdbi

  GNU R Annotation Database Interface for BioConductor

• sug: r-bioc-biocgenerics

  generic functions for Bioconductor

• sug: r-bioc-biomart

  GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

• sug: r-bioc-biomformat

  GNU R interface package for the BIOM file format

• sug: r-bioc-biovizbase

  GNU R basic graphic utilities for visualization of genomic data

• sug: r-bioc-bsgenome

  BioConductor infrastructure for Biostrings-based genome data packages

• sug: r-bioc-genomeinfodb

  BioConductor utilities for manipulating chromosome identifiers

• sug: r-bioc-genomicalignments

  BioConductor representation and manipulation of short genomic alignments

• sug: r-bioc-genomicfeatures

  GNU R tools for making and manipulating transcript centric annotations

• sug: r-bioc-genomicranges

  BioConductor representation and manipulation of genomic intervals

• sug: r-bioc-graph

  handle graph data structures for BioConductor

• sug: r-bioc-hypergraph

  BioConductor hypergraph data structures

• sug: r-bioc-iranges

  GNU R low-level containers for storing sets of integer ranges

• sug: r-bioc-makecdfenv

  BioConductor CDF Environment Maker

• sug: r-bioc-preprocesscore

  BioConductor collection of pre-processing functions

• sug: r-bioc-rbgl

  R interface to the graph algorithms contained in the BOOST library

• sug: r-bioc-rsamtools

  GNU R binary alignment (BAM), variant call (BCF), or tabix file import

• sug: r-bioc-shortread

  GNU R classes and methods for high-throughput short-read sequencing data

• sug: r-bioc-snpstats

  BioConductor SnpMatrix and XSnpMatrix classes and methods

• sug: r-bioc-variantannotation

  BioConductor annotation of genetic variants

• sug: r-bioc-xvector

  BioConductor representation and manpulation of external sequences

• sug: r-cran-natserv

  GNU R 'NatureServe' Interface

• sug: r-cran-rentrez

  GNU R interface to the NCBI's EUtils API

• sug: r-cran-rocr

  GNU R package to prepare and display ROC curves

• sug: ruby-rgfa

  parse, edit and write GFA format graphs in Ruby

• sug: vdjtools

  Package not available

Download med-bio-dev

Download for all available architectures

Architecture	Package Size	Installed Size	Files
all	17.2 kB	40.0 kB	[list of files]