Package: med-bio-dev (3.8.2)

[ 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 (= 3.8.2)

  Debian Med general config package

• dep: med-tasks (= 3.8.2)

  tarefas Debian Med para tasksel

• rec: bio-tradis

  analyse the output from TraDIS analyses of genomic sequences

• rec: biobambam2

  tools for early stage alignment file processing

• rec: bioperl

  Ferramentas Perl para biologia molecular computacional

• 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: goby-java

  next-generation sequencing data and results analysis tool

• 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: libbigwig-dev

  C library for handling bigWig files - header files

• rec: libbio-alignio-stockholm-perl

  stockholm sequence input/output stream

• 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-cluster-perl

  BioPerl cluster modules

• rec: libbio-coordinate-perl

  BioPerl modules for working with biological coordinates

• rec: libbio-das-lite-perl

  implementation of the BioDas protocol

• rec: libbio-db-biofetch-perl

  Database object interface to BioFetch retrieval

• rec: libbio-db-embl-perl

  Database object interface for EMBL entry retrieval

• rec: libbio-db-hts-perl

  Perl interface to the HTS library

• rec: libbio-db-ncbihelper-perl

  collection of routines useful for queries to NCBI databases

• rec: libbio-db-seqfeature-perl

  Normalized feature for use with Bio::DB::SeqFeature::Store

• rec: libbio-eutilities-perl

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

• rec: libbio-featureio-perl

  Modules for reading, writing, and manipulating sequence features

• 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: libbio-tools-run-remoteblast-perl

  Object for remote execution of the NCBI Blast via HTTP

• rec: libbio-variation-perl

  BioPerl variation-related functionality

• rec: libbiojava-java

  Java API to biological data and applications (default version)

• rec: libbiojava6-java

  Java API to biological data and applications (version 6)

• 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: libcifpp-dev

  Documentation for libcifpp

• 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: libgatbcore-dev

  development library of the Genome Analysis Toolbox

• rec: libgclib-dev

  header files for Genome Code Lib (GCLib)

• 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: libhdf5-dev

  HDF5 - development files - serial version

• rec: libhmsbeagle-dev

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

• rec: libhts-dev

  development files for the HTSlib

• rec: libhtscodecs-dev

  Development headers for custom compression for CRAM and others

• 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: libminimap2-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: libnhgri-blastall-perl

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

• rec: libopenmm-dev

  C++ header files for the OpenMM library

• rec: libopenms-dev

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

• rec: libpal-java

  Phylogenetic Analysis Library

• rec: libparasail-dev

  Development heaaders and static libraries for parasail

• 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: libpdb-redo-dev

  Development files for libpdb-redo

• rec: libpll-dev

  Phylogenetic Likelihood Library (development)

• rec: libpwiz-dev

  library to perform proteomics data analyses (devel files)

• rec: libqes-dev

  DNA sequence parsing library -- development

• rec: librcsb-core-wrapper0-dev

  development files for librcsb-core-wrapper0t64

• rec: librdp-taxonomy-tree-java

  taxonomy tree library from Ribosomal Database Project (RDP)

• 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: libseqan3-dev

  C++ library for the analysis of biological sequences v3 (development)

• rec: libseqlib-dev

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

• rec: libslow5-dev

  header and static library for reading & writing SLOW5 files

• 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: libssu-dev

  high-performance phylogenetic diversity calculations (dev)

• 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: libthread-pool-dev

  C++ header-only thread pool library (devel)

• rec: libvcflib-dev

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

• rec: libvibrant6-dev

  bibliotecas NCBI para aplicações gráficas de biologia (arquivos de desenvolvimento)

• rec: libwfa2-dev

  exact gap-affine algorithm (development)

• 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: nim-hts-dev

  wrapper for hts C library

• rec: nim-kexpr-dev

  kexpr math expressions for nim

• rec: nim-lapper-dev

  simple, fast interval searches for nim

• rec: ont-fast5-api

  simple interface to HDF5 files of the Oxford Nanopore .fast5 file format

• rec: pyfai

  Fast Azimuthal Integration scripts

• rec: python3-airr

  Data Representation Standard library for antibody and TCR sequences

• rec: python3-anndata

  annotated gene by sample numpy matrix

• rec: python3-bcbio-gff

  Python3 library to read and write Generic Feature Format

• rec: python3-bioframe

  library to enable flexible, scalable operations on genomic interval dataframes

• 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-cigar

  manipulate SAM cigar strings

• rec: python3-cobra

  constraint-based modeling of biological networks with Python 3

• rec: python3-cogent3

  framework for genomic biology

• rec: python3-cooler

  library for a sparse, compressed, binary persistent storage

• rec: python3-corepywrap

  library that exports C++ mmCIF accessors to Python3

• 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-deeptools

  platform for exploring biological deep-sequencing data

• rec: python3-deeptoolsintervals

  handlig GTF-like sequence-associated interal-annotation

• 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-ete3

  Python Environment for (phylogenetic) Tree Exploration - Python 3.X

• 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-gtfparse

  parser for gene transfer format (aka GFF2)

• rec: python3-htseq

  Python3 high-throughput genome sequencing read analysis utilities

• rec: python3-intervaltree-bio

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

• rec: python3-kineticstools

  detection of DNA modifications (Python 3 library)

• rec: python3-loompy

  access loom formatted files for bioinformatics

• rec: python3-mirtop

  annotate miRNAs with a standard mirna/isomir naming (Python 3)

• rec: python3-nanoget

  extract information from Oxford Nanopore sequencing data and alignments

• rec: python3-ngs

  Next Generation Sequencing language Bindings (Python3 bindings)

• rec: python3-pairix

  1D/2D indexing and querying with a pair of genomic coordinates

• rec: python3-pangolearn

  store of the trained model for pangolin to access

• rec: python3-parasail

  Python3 bindings for the parasail C library

• rec: python3-pbcommand

  common command-line interface for Pacific Biosciences analysis modules

• rec: python3-pbconsensuscore

  algorithms for PacBio multiple sequence consensus -- Python 3

• rec: python3-pbcore

  Python 3 library for processing PacBio data files

• rec: python3-peptidebuilder

  generate atomic oligopeptide 3D structure from sequence

• rec: python3-presto

  toolkit for processing B and T cell sequences (Python3 module)

• rec: python3-propka

  heuristic pKa calculations with ligands (Python 3)

• rec: python3-py2bit

  access to 2bit files

• rec: python3-pyabpoa

  adaptive banded Partial Order Alignment - python3 module

• rec: python3-pyani

  Python3 module for average nucleotide identity analyses

• rec: python3-pybedtools

  Python 3 wrapper around BEDTools for bioinformatics work

• rec: python3-pybel

  Biological Expression Language

• rec: python3-pybigwig

  Python 3 module for quick access to bigBed and bigWig files

• rec: python3-pyfaidx

  efficient random access to fasta subsequences for Python 3

• rec: python3-pyfastx

  fast random access to sequences from FASTA/Q file - python3 module

• rec: python3-pymummer

  Python 3 interface to MUMmer

• rec: python3-pyranges

  2D representation of genomic intervals and their annotations

• rec: python3-pysam

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

• rec: python3-pyspoa

  Python bindings to spoa

• 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-shasta

  nanopore whole genome assembly (dynamic library)

• rec: python3-skbio

  Python3 data structures, algorithms, educational resources for bioinformatic

• rec: python3-slow5

  Python3 modul for reading & writing SLOW5 files

• rec: python3-sqt

  SeQuencing Tools for biological DNA/RNA high-throughput data

• rec: python3-streamz

  build pipelines to manage continuous streams of data

• rec: python3-tinyalign

  numerical representation of differences between strings

• rec: python3-torch

  Tensors and Dynamic neural networks in Python (Python Interface)

• rec: python3-treetime

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

• rec: python3-unifrac

  high-performance phylogenetic diversity calculations

• rec: python3-wdlparse

  Workflow Description Language (WDL) parser for Python

• rec: r-bioc-biobase

  base functions for Bioconductor

• rec: r-cran-boolnet

  assembling, analyzing and visualizing Boolean networks

• rec: r-cran-corrplot

  Visualization of a Correlation Matrix

• 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-gprofiler2

  Interface to the 'g:Profiler' Toolset

• rec: r-cran-haplo.stats

  GNU R package for haplotype analysis

• 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-sctransform

  Variance Stabilizing Transformations for Single Cell UMI Data

• rec: r-cran-seqinr

  GNU R biological sequences retrieval and analysis

• rec: r-cran-seurat

  Tools for Single Cell Genomics

• rec: r-cran-tsne

  t-distributed stochastic neighbor embedding for R (t-SNE)

• rec: r-cran-vegan

  Community Ecology Package for R

• rec: r-cran-webgestaltr

  find over-represented properties in gene lists

• 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: snakemake

  pythonic workflow management system

• rec: toil

  cross-platform workflow engine

• sug: bioclipse

  Package not available

• sug: capsule-nextflow

  packaging and deployment tool for Java applications

• sug: conda-package-handling

  create and extract conda packages of various formats

• sug: ctdconverter

  Convert CTD files into Galaxy tool and CWL CommandLineTool files

• sug: cthreadpool-dev

  minimal ANSI C thread pool - development files

• sug: cwlformat

  code formatter for Common Workflow Language

• sug: cwltest

  Common Workflow Language testing framework

• sug: libargs-dev

  simple header-only C++ argument parser library

• sug: libatomicqueue-dev

  Package not available

• sug: libbam-dev

  manipulates nucleotide sequence alignments in BAM or SAM format

• sug: libbbhash-dev

  bloom-filter based minimal perfect hash function library

• sug: libbifrost-dev

  static library and header files for libbifrost

• sug: libbiojava4-java

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

• sug: libbiosoup-dev

  C++ header-only support library for bioinformatics tools

• sug: libbtllib-dev

  Bioinformatics Technology Lab common code library

• sug: libcapsule-maven-nextflow-java

  packaging tool for Java applications with Maven coordinates

• sug: libconcurrentqueue-dev

  industrial-strength lock-free queue for C++

• 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-dev

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

• sug: libfreecontact-doc

  documentation for libfreecontact

• sug: libfreecontact-perl

  fast protein contact predictor - binding for Perl

• sug: libgatk-bwamem-java

  interface to call Heng Li's bwa mem aligner from Java code

• sug: libgatk-bwamem-jni

  interface to call Heng Li's bwa mem aligner from Java code (jni)

• sug: libgatk-fermilite-java

  interface to call Heng Li's fermi-lite assembler from Java code

• sug: libgatk-fermilite-jni

  interface to call Heng Li's fermi-lite assembler from Java code (jni)

• sug: libgatk-native-bindings-java

  library of native bindings for gatk and picard-tools

• sug: libgenomicsdb-dev

  sparse array storage library for genomics (development files)

• sug: libgenomicsdb-java

  sparse array storage library for genomics (Java library)

• sug: libicb-utils-java

  Java library of utilities to manage files and compute statistics

• sug: libmaus2-dev

  collection of data structures and algorithms for biobambam (devel)

• sug: libmilib-java

  library for Next Generation Sequencing (NGS) data processing

• sug: libminimap-dev

  development headers for libminimap

• sug: libmmblib-dev

  Package not available

• sug: libmodhmm-dev

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

• sug: libnexml-java

  Package not available

• sug: libngs-sdk-dev

  Package not available

• sug: libpbcopper-dev

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

• sug: libqcpp-dev

  Package not available

• sug: librelion-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: libsavvy-dev

  C++ interface for the SAV file format

• sug: libsuma-dev

  headers and static library for sumatra and sumaclust

• sug: libsvmloc-dev

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

• sug: libswarm2-dev

  Package not available

• sug: libterraces-dev

  enumerate terraces in phylogenetic tree space (development lib)

• sug: libtfbs-perl

  scanning DNA sequence with a position weight matrix

• sug: libvbz-hdf-plugin-dev

  VBZ compression plugin for nanopore signal data (devel)

• sug: libxxsds-dynamic-dev

  succinct and compressed fully-dynamic data structures library

• sug: octace-bioinfo

  Package not available

• sug: python-biopython-doc

  Documentation for the Biopython library

• sug: python3-alignlib

  edit and Hamming distances for biological sequences

• sug: python3-bcbio

  library for analysing high-throughput sequencing data

• sug: python3-bel-resources

  Python3 utilities for BEL resource files

• sug: python3-bioblend

  CloudMan and Galaxy API library (Python 3)

• sug: python3-biopython-sql

  Biopython support for the BioSQL database schema (Python 3)

• sug: python3-cgelib

  Python3 code to be utilized across the CGE tools

• sug: python3-compclust

  Package not available

• sug: python3-conda-package-streaming

  fetch conda metadata

• sug: python3-consensuscore2

  Package not available

• sug: python3-ctdopts

  Gives your Python tools a CTD-compatible interface

• sug: python3-galaxy-lib

  Package not available

• sug: python3-intake

  lightweight package for finding and investigating data

• sug: python3-joypy

  ridgeline-/joyplots plotting routine

• sug: python3-misopy

  Package not available

• sug: python3-ncls

  datastructure for interval overlap queries

• sug: python3-networkx

  tool to create, manipulate and study complex networks (Python3)

• sug: python3-pycosat

  Python bindings to picosat

• sug: python3-pyflow

  lightweight parallel task engine for Python

• sug: python3-roadrunner

  Package not available

• sug: python3-scanpy

  Package not available

• sug: python3-seqcluster

  analysis of small RNA in NGS data

• sug: q2-alignment

  QIIME 2 plugin for generating and manipulating alignments

• sug: q2-composition

  Package not available

• sug: q2-cutadapt

  QIIME 2 plugin to work with adapters in sequence data

• sug: q2-dada2

  QIIME 2 plugin to work with adapters in sequence data

• sug: q2-deblur

  Package not available

• sug: q2-demux

  QIIME 2 plugin for demultiplexing of sequence reads

• sug: q2-diversity

  Package not available

• sug: q2-emperor

  QIIME2 plugin for display of ordination plots

• sug: q2-feature-classifier

  QIIME 2 plugin supporting taxonomic classification

• sug: q2-feature-table

  QIIME 2 plugin supporting operations on feature tables

• sug: q2-fragment-insertion

  QIIME 2 plugin for fragment insertion

• sug: q2-gneiss

  Package not available

• sug: q2-longitudinal

  Package not available

• sug: q2-metadata

  QIIME 2 plugin for working with and visualizing Metadata

• sug: q2-phylogeny

  QIIME 2 plugin for phylogeny

• sug: q2-quality-control

  QIIME 2 plugin for quality assurance of feature and sequence data

• sug: q2-quality-filter

  QIIME2 plugin for PHRED-based filtering and trimming

• sug: q2-sample-classifier

  QIIME 2 plugin for machine learning prediction of sample data

• sug: q2-shogun

  Package not available

• sug: q2-taxa

  QIIME 2 plugin for working with feature taxonomy annotations

• sug: q2-types

  QIIME 2 plugin defining types for microbiome analysis

• sug: q2-vsearch

  Package not available

• sug: q2cli

  Click-based command line interface for QIIME 2

• sug: q2cwl

  Package not available

• sug: q2lint

  Package not available

• sug: q2templates

  Design template package for QIIME 2 Plugins

• sug: qiime

  Quantitative Insights Into Microbial Ecology

• sug: r-bioc-affxparser

  Affymetrix File Parsing SDK

• 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-arrayexpress

  access to the ArrayExpress Microarray Database at EBI

• sug: r-bioc-biocgenerics

  generic functions for Bioconductor

• sug: r-bioc-biocneighbors

  Nearest Neighbor Detection for Bioconductor Packages

• 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

  Package not available

• sug: r-bioc-bridgedbr

  Package not available

• sug: r-bioc-bsgenome

  BioConductor infrastructure for Biostrings-based genome data packages

• sug: r-bioc-cager

  Package not available

• sug: r-bioc-cner

  CNE Detection and Visualization

• sug: r-bioc-complexheatmap

  make complex heatmaps using GNU R

• sug: r-bioc-ctc

  Cluster and Tree Conversion

• 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-enrichedheatmap

  Package not available

• 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-gseabase

  Gene set enrichment data structures and methods

• sug: r-bioc-gsva

  Gene Set Variation Analysis for microarray and RNA-seq data

• 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

  GNU R statistical analysis for sparse high-throughput sequencing

• sug: r-bioc-mofa

  Multi-Omics Factor Analysis (MOFA)

• sug: r-bioc-multiassayexperiment

  Software for integrating multi-omics experiments in BioConductor

• sug: r-bioc-nanostringqcpro

  Package not available

• sug: r-bioc-oligo

  Preprocessing tools for oligonucleotide arrays

• sug: r-bioc-oligoclasses

  Classes for high-throughput arrays supported by oligo and crlmm

• sug: r-bioc-org.hs.eg.db

  genome-wide annotation for Human

• 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-purecn

  copy number calling and SNV classification using targeted short read sequencing

• 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-s4vectors

  BioConductor S4 implementation of vectors and lists

• 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-structuralvariantannotation

  Variant annotations for structural variants

• sug: r-bioc-tfbstools

  GNU R Transcription Factor Binding Site (TFBS) Analysis

• sug: r-bioc-titancna

  Subclonal copy number and LOH prediction from whole genome sequencing

• 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-adegenet

  GNU R exploratory analysis of genetic and genomic data

• sug: r-cran-adephylo

  GNU R exploratory analyses for the phylogenetic comparative method

• sug: r-cran-amap

  Another Multidimensional Analysis Package

• sug: r-cran-biwt

  biweight mean vector and covariance and correlation

• 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-fastcluster

  Fast hierarchical clustering routines for GNU R

• 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-itertools

  Iterator Tools

• sug: r-cran-kaos

  Encoding of Sequences Based on Frequency Matrix Chaos

• sug: r-cran-metap

  Meta-Analysis of Significance Values

• sug: r-cran-minerva

  Maximal Information-Based Nonparametric Exploration

• sug: r-cran-natserv

  GNU R 'NatureServe' Interface

• sug: r-cran-nmf

  GNU R framework to perform non-negative matrix factorization

• sug: r-cran-optimalcutpoints

  Computing Optimal Cutpoints in Diagnostic Tests

• sug: r-cran-parmigene

  Parallel Mutual Information to establish Gene Networks

• 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-rcpphnsw

  R bindings for a Library for Approximate Nearest Neighbors

• sug: r-cran-robustrankaggreg

  Methods for robust rank aggregation

• sug: r-cran-rocr

  GNU R package to prepare and display ROC curves

• sug: r-cran-rook

  web server interface for R

• sug: r-cran-rsvd

  Randomized Singular Value Decomposition

• sug: r-cran-shazam

  Immunoglobulin Somatic Hypermutation Analysis

• sug: r-cran-sitmo

  GNU R parallel pseudo random number generator 'sitmo' header files

• sug: r-cran-venndiagram

  Generate High-Resolution Venn and Euler Plots

• 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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