Package: med-bio-dev (3.5.1) [universe]

Links for med-bio-dev

Ubuntu Resources:

Download Source Package debian-med:

Maintainer:

Ubuntu MOTU Developers (Mail Archive)

Please consider filing a bug or asking a question via Launchpad before contacting the maintainer directly.

Original Maintainers (usually from Debian):

Debian Med Packaging Team (Mail Archive)
Andreas Tille

It should generally not be necessary for users to contact the original maintainer.

Similar packages:

Debian Med packages for development of bioinformatics applications

Other Packages Related to med-bio-dev

depends

recommends

suggests

enhances

dep: med-config (= 3.5.1)

Debian Med general config package
dep: med-tasks (= 3.5.1)

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: gffread

GFF/GTF format conversions, region filtering, FASTA sequence extraction
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: libcdk-java

Chemistry Development Kit (CDK) Java libraries
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

Package not available
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: libseqan2-dev

C++ library for the analysis of biological sequences (development)
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: python3-airr

Data Representation Standard library for antibody and TCR sequences
rec: python3-bcbio

Package not available
rec: python3-biom-format

Biological Observation Matrix (BIOM) format (Python 3)
rec: python3-biomaj3

BioMAJ workflow management library
rec: python3-biopython

Python3 library for bioinformatics
rec: python3-biotools

Python3 bioinformatics utilities for high-throughput genomic sequencing
rec: python3-bx

library to manage genomic data and its alignment
rec: python3-cgecore

Python3 module for the Center for Genomic Epidemiology
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-dnaio

Python 3 library for fast parsing of FASTQ and FASTA files
rec: python3-fast5

library for reading Oxford Nanopore Fast5 files -- Python 3
rec: python3-freecontact

fast protein contact predictor - binding for Python3
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-htseq

Python3 high-throughput genome sequencing read analysis utilities
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-py2bit

access to 2bit files
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

virtual package provided by python3-vcf
rec: python3-rdkit

Collection of cheminformatics and machine-learning software
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-adegenet

GNU R exploratory analysis of genetic and genomic data
rec: r-cran-adephylo

GNU R exploratory analyses for the phylogenetic comparative method
rec: r-cran-boolnet

assembling, analyzing and visualizing Boolean networks
rec: r-cran-distory

GNU R distance between phylogenetic histories
rec: r-cran-fitdistrplus

support fit of parametric distribution
rec: r-cran-forecast

GNU R forecasting functions for time series and linear models
rec: r-cran-genetics

GNU R package for population genetics
rec: r-cran-gprofiler

Interface to the 'g:Profiler' Toolkit
rec: r-cran-haplo.stats

GNU R package for haplotype analysis
rec: r-cran-metamix

GNU R bayesian mixture analysis for metagenomic community profiling
rec: r-cran-phangorn

GNU R package for phylogenetic analysis
rec: r-cran-pheatmap

GNU R package to create pretty heatmaps
rec: r-cran-phylobase

GNU R base package for phylogenetic structures and comparative data
rec: r-cran-pscbs

R package: Analysis of Parent-Specific DNA Copy Numbers
rec: r-cran-qqman

R package for visualizing GWAS results using Q-Q and manhattan plots
rec: r-cran-rentrez

GNU R interface to the NCBI's EUtils API
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: r-cran-rotl

GNU R interface to the 'Open Tree of Life' API
rec: r-cran-samr

GNU R significance analysis of microarrays
rec: r-cran-seqinr

GNU R biological sequences retrieval and analysis
rec: r-cran-vegan

Community Ecology Package for R
rec: r-cran-webgestaltr

find over-represented properties in gene lists
rec: r-other-hms-dbmi-spp

virtual package provided by r-cran-spp
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: biobambam2

tools for early stage alignment file processing
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

C library for handling bigWig files - header files
sug: libbiod-dev

bioinformatics library in D (development files)
sug: libdisorder-dev

library for entropy measurement of byte streams (devel)
sug: libfast-perl

Package not available
sug: libforester-java

Package not available
sug: libfreecontact-doc

documentation for libfreecontact
sug: libgclib

Package not available
sug: libgoby-java

Package not available
sug: libmaus2-dev

collection of data structures and algorithms for biobambam (devel)
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: libseqan3-dev

C++ library for the analysis of biological sequences v3 (development)
sug: libsvmloc-dev

PSORTb adapted library for svm machine-learning library (dev)
sug: libswarm2-dev

Package not available
sug: mgltools-networkeditor

Package not available
sug: mgltools-pybabel

Package not available
sug: mgltools-vision

Package not available
sug: octace-bioinfo

Package not available
sug: pyfai

Fast Azimuthal Integration scripts
sug: python-biopython-doc

Documentation for the Biopython library
sug: python-cogent

Package not available
sug: python-corepywrap

Package not available
sug: python-kineticstools

Package not available
sug: python-pbcommand

Package not available
sug: python-pbcore

virtual package provided by python3-pbcore
sug: python-pbh5tools

Package not available
sug: python3-alignlib

edit and Hamming distances for biological sequences
sug: python3-biopython-sql

Biopython support for the BioSQL database schema (Python 3)
sug: python3-consensuscore2

Package not available
sug: python3-ctdopts

Gives your Python tools a CTD-compatible interface
sug: python3-deeptools

platform for exploring biological deep-sequencing data
sug: python3-deeptoolsintervals

handlig GTF-like sequence-associated interal-annotation
sug: python3-ete3

Package not available
sug: python3-hyphy

Package not available
sug: python3-intervaltree-bio

Interval tree convenience classes for genomic data -- Python 3 library
sug: python3-loompy

Package not available
sug: python3-mirtop

annotate miRNAs with a standard mirna/isomir naming (Python 3)
sug: python3-misopy

Package not available
sug: python3-pyani

Python3 module for average nucleotide identity analyses
sug: python3-pycosat

Python bindings to picosat
sug: python3-pyflow

lightweight parallel task engine for Python
sug: python3-roadrunner

Package not available
sug: python3-seqcluster

Package not available
sug: python3-skbio

Python3 data structures, algorithms, educational resources for bioinformatic
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-annotate

BioConductor annotation for microarrays
sug: r-bioc-annotationdbi

GNU R Annotation Database Interface for BioConductor
sug: r-bioc-annotationhub

GNU R client to access AnnotationHub resources
sug: r-bioc-aroma.light

BioConductor methods normalization and visualization of microarray data
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-biostrings

GNU R string objects representing biological sequences
sug: r-bioc-biovizbase

GNU R basic graphic utilities for visualization of genomic data
sug: r-bioc-bitseq

transcript expression inference and analysis for RNA-seq data
sug: r-bioc-bsgenome

BioConductor infrastructure for Biostrings-based genome data packages
sug: r-bioc-cner

CNE Detection and Visualization
sug: r-bioc-cummerbund

tool for analysis of Cufflinks RNA-Seq output
sug: r-bioc-dada2

sample inference from amplicon sequencing data
sug: r-bioc-deseq2

R package for RNA-Seq Differential Expression Analysis
sug: r-bioc-dnacopy

R package: DNA copy number data analysis
sug: r-bioc-ebseq

R package for RNA-Seq Differential Expression Analysis
sug: r-bioc-ensembldb

GNU R utilities to create and use an Ensembl based annotation database
sug: r-bioc-genefilter

methods for filtering genes from microarray experiments
sug: r-bioc-geneplotter

R package of functions for plotting genomic data
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-geoquery

Get data from NCBI Gene Expression Omnibus (GEO)
sug: r-bioc-go.db

annotation maps describing the entire Gene Ontology
sug: r-bioc-graph

handle graph data structures for BioConductor
sug: r-bioc-gviz

Plotting data and annotation information along genomic coordinates
sug: r-bioc-hypergraph

BioConductor hypergraph data structures
sug: r-bioc-impute

Imputation for microarray data
sug: r-bioc-iranges

GNU R low-level containers for storing sets of integer ranges
sug: r-bioc-limma

linear models for microarray data
sug: r-bioc-makecdfenv

BioConductor CDF Environment Maker
sug: r-bioc-mergeomics

Integrative network analysis of omics data
sug: r-bioc-metagenomeseq

Package not available
sug: r-bioc-mofa

Package not available
sug: r-bioc-multiassayexperiment

Software for integrating multi-omics experiments in BioConductor
sug: r-bioc-pcamethods

BioConductor collection of PCA methods
sug: r-bioc-phyloseq

GNU R handling and analysis of high-throughput microbiome census data
sug: r-bioc-preprocesscore

BioConductor collection of pre-processing functions
sug: r-bioc-qusage

qusage: Quantitative Set Analysis for Gene Expression
sug: r-bioc-rbgl

R interface to the graph algorithms contained in the BOOST library
sug: r-bioc-rentrez

Package not available
sug: r-bioc-rsamtools

GNU R binary alignment (BAM), variant call (BCF), or tabix file import
sug: r-bioc-rtracklayer

GNU R interface to genome browsers and their annotation tracks
sug: r-bioc-savr

GNU R parse and analyze Illumina SAV files
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-tfbstools

GNU R Transcription Factor Binding Site (TFBS) Analysis
sug: r-bioc-tximport

transcript-level estimates for biological sequencing
sug: r-bioc-variantannotation

BioConductor annotation of genetic variants
sug: r-bioc-xvector

BioConductor representation and manpulation of external sequences
sug: r-cran-corrplot

Visualization of a Correlation Matrix
sug: r-cran-drinsight

Package not available
sug: r-cran-dt

GNU R wrapper of the JavaScript library 'DataTables'
sug: r-cran-dynamictreecut

Methods for Detection of Clusters in Hierarchical Clustering
sug: r-cran-future.apply

apply function to elements in parallel using futures
sug: r-cran-future.batchtools

Future API for Parallel and Distributed Processing
sug: r-cran-ica

Independent Component Analysis
sug: r-cran-kaos

Encoding of Sequences Based on Frequency Matrix Chaos
sug: r-cran-metap

Meta-Analysis of Significance Values
sug: r-cran-natserv

GNU R 'NatureServe' Interface
sug: r-cran-pcapp

Robust PCA by Projection Pursuit
sug: r-cran-proc

Display and Analyze ROC Curves
sug: r-cran-rann

Fast Nearest Neighbour Search Using L2 Metric
sug: r-cran-rocr

GNU R package to prepare and display ROC curves
sug: r-cran-rsvd

Randomized Singular Value Decomposition
sug: r-cran-sctransform

Variance Stabilizing Transformations for Single Cell UMI Data
sug: r-cran-seurat

Tools for Single Cell Genomics
sug: r-cran-tsne

t-distributed stochastic neighbor embedding for R (t-SNE)
sug: r-other-apmswapp

Package not available
sug: ruby-rgfa

parse, edit and write GFA format graphs in Ruby
sug: vdjtools

framework for post-analysis of B/T cell repertoires

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