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  biotoolsCURIE: biotools:fusion
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  description: Web application for the integrative analysis of omics data providing
    a collection of new and established tools and visualization methods to support
    researchers in exploring multi-level omics data. The software focuses on data-rich
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    and offers convenient functionality for a) omics data manipulation, b) data analysis,
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    note: null
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  publication:
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    metadata:
      abstract: 'We present Omics Fusion, a new web-based platform for integrative
        analysis of omics data. Omics Fusion provides a collection of new and established
        tools and visualization methods to support researchers in exploring omics
        data, validating results or understanding how to adjust experiments in order
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        are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de/.'
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      - name: Seidel A.
      - name: Kleinbolting N.
      - name: Nattkemper T.W.
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      citationCount: 9
      date: '2016-12-18T00:00:00Z'
      journal: Journal of integrative bioinformatics
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    note: null
    pmcid: null
    pmid: '28187412'
    type:
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    version: null
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  toolType:
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  - term: Protein expression
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  - term: Gene expression
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  validated: 1
  version: []
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  description: Differential quantification of alternative splicing events on spliced
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  description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
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      format:
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      format:
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    note: null
    operation:
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    output:
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      format:
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  language:
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  link:
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    type:
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    metadata: null
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    type: uses
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    type: uses
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    type: uses
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    type: uses
  - biotoolsID: deepsig
    type: uses
  toolType:
  - Web application
  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_0622
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    uri: http://edamontology.org/topic_0080
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    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
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  additionDate: '2023-06-07T03:22:25.847061Z'
  biotoolsCURIE: biotools:metabuli
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  description: 'Metabuli: specific and sensitive metagenomic classification via joint
    analysis of DNA and amino acid'
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  function:
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    input:
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    note: null
    operation:
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      uri: http://edamontology.org/operation_3460
    output: []
  homepage: https://metabuli.steineggerlab.com
  homepage_status: 0
  language:
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  lastUpdate: '2026-01-28T15:27:48.519515Z'
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    type:
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  otherID: []
  owner: milot-mirdita
  publication:
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    metadata:
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      date: '2024-06-01T00:00:00Z'
      journal: Nature Methods
      title: 'Metabuli: sensitive and specific metagenomic classification via joint
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  - doi: 10.1101/2023.05.31.543018
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  - doi: 10.1093/bioinformatics/btaf557
    metadata:
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      date: '2025-10-02T00:00:00Z'
      journal: Bioinformatics (Oxford, England)
      title: Easy and interactive taxonomic profiling with Metabuli App
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  relation:
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    type: uses
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  topic:
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    uri: http://edamontology.org/topic_0637
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-02-11T12:02:14Z'
  biotoolsCURIE: biotools:motus
  biotoolsID: motus
  collectionID:
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  cost: Free of charge
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    fundrefid: null
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    name: European Molecular Biology Laboratory (EMBL)
    note: null
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  description: Metagenomic operational taxonomic units (mOTUs) enable high-accuracy
    taxonomic profiling of known (sequenced) and unknown microorganisms at species-level
    resolution from shotgun metagenomic or metatranscriptomic data. The method clusters
    single-copy phylogenetic marker gene sequences from metagenomes and reference
    genomes into mOTUs to quantify their abundances in meta-omics data with very high
    precision and recall.
  documentation:
  - note: null
    type:
    - General
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  download:
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    type: Biological data
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    input:
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      format:
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    note: Taxonomic profiling from shotgun metagenomes Quality-filtered shotgun metagenomic
      reads A taxonomic profiling matrix with species in rows and samples in columns;
      each entry m_{i,j} indicates the number of reads from sample j mapped to marker
      genes of species i
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
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      format:
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  homepage: https://motu-tool.org/
  homepage_status: 0
  language:
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  license: GPL-3.0
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  - note: null
    type:
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    url: http://www.bork.embl.de/software/mOTU/download.html
  maturity: null
  name: Metagenomic operational taxonomic units (mOTUs)
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  owner: hdhub
  publication:
  - doi: 10.1038/nmeth.2693
    metadata:
      abstract: To quantify known and unknown microorganisms at species-level resolution
        using shotgun sequencing data, we developed a method that establishes metagenomic
        operational taxonomic units (mOTUs) based on single-copy phylogenetic marker
        genes. Applied to 252 human fecal samples, the method revealed that on average
        43% of the species abundance and 58% of the richness cannot be captured by
        current reference genome-based methods. An implementation of the method is
        available at http://www.bork.embl.de/software/mOTU/. © 2013 Nature America,
        Inc.
      authors:
      - name: Sunagawa S.
      - name: Mende D.R.
      - name: Zeller G.
      - name: Izquierdo-Carrasco F.
      - name: Berger S.A.
      - name: Kultima J.R.
      - name: Coelho L.P.
      - name: Arumugam M.
      - name: Tap J.
      - name: Nielsen H.B.
      - name: Rasmussen S.
      - name: Brunak So.
      - name: Pedersen O.
      - name: Guarner F.
      - name: De Vos W.M.
      - name: Wang J.
      - name: Li J.
      - name: Dore J.
      - name: Dusko Ehrlich S.
      - name: Stamatakis A.
      - name: Bork P.
      citationCount: 367
      date: '2013-12-01T00:00:00Z'
      journal: Nature Methods
      title: Metagenomic species profiling using universal phylogenetic marker genes
    note: null
    pmcid: null
    pmid: '24141494'
    type:
    - Primary
    version: null
  - doi: 10.1038/s41467-019-08844-4
    metadata:
      abstract: Metagenomic sequencing has greatly improved our ability to profile
        the composition of environmental and host-associated microbial communities.
        However, the dependency of most methods on reference genomes, which are currently
        unavailable for a substantial fraction of microbial species, introduces estimation
        biases. We present an updated and functionally extended tool based on universal
        (i.e., reference-independent), phylogenetic marker gene (MG)-based operational
        taxonomic units (mOTUs) enabling the profiling of >7700 microbial species.
        As more than 30% of them could not previously be quantified at this taxonomic
        resolution, relative abundance estimates based on mOTUs are more accurate
        compared to other methods. As a new feature, we show that mOTUs, which are
        based on essential housekeeping genes, are demonstrably well-suited for quantification
        of basal transcriptional activity of community members. Furthermore, single
        nucleotide variation profiles estimated using mOTUs reflect those from whole
        genomes, which allows for comparing microbial strain populations (e.g., across
        different human body sites).
      authors:
      - name: Milanese A.
      - name: Mende D.R.
      - name: Paoli L.
      - name: Salazar G.
      - name: Ruscheweyh H.-J.
      - name: Cuenca M.
      - name: Hingamp P.
      - name: Alves R.
      - name: Costea P.I.
      - name: Coelho L.P.
      - name: Schmidt T.S.B.
      - name: Almeida A.
      - name: Mitchell A.L.
      - name: Finn R.D.
      - name: Huerta-Cepas J.
      - name: Bork P.
      - name: Zeller G.
      - name: Sunagawa S.
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  - email: pamela.guevara@biomedica.udec.cl
    fundrefid: null
    gridid: null
    name: Pamela Guevara
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Phybers is a Python library for analyzing brain tractography data,
    offering tools for segmentation, clustering, visualization, and normalization.
    It is freely available on GitHub under the GNU public license and provides extensive
    documentation and sample data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output: []
  homepage: https://phybers.github.io/phybers
  homepage_status: 0
  language:
  - C++
  - Python
  - C
  lastUpdate: '2026-01-14T15:38:32.082307Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: Phybers
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.3389/FNINS.2024.1333243
    metadata: null
    note: null
    pmcid: PMC10962387
    pmid: '38529266'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Neurobiology
    uri: http://edamontology.org/topic_3304
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
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