count: 4608
list:
- accessibility: Open access
  additionDate: '2019-05-27T16:59:15Z'
  biotoolsCURIE: biotools:SLiM_software
  biotoolsID: SLiM_software
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: messer@cornell.edu
    fundrefid: null
    gridid: null
    name: Philipp Messer
    note: null
    orcidid: https://orcid.org/0000-0001-8453-9377
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://messerlab.org
  - email: bhaller@benhaller.com
    fundrefid: null
    gridid: null
    name: Benjamin C. Haller
    note: null
    orcidid: https://orcid.org/0000-0003-1874-8327
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://benhaller.com
  description: Evolutionary simulation framework that combines a powerful engine for
    population genetic simulations with the capability of modeling arbitrarily complex
    evolutionary scenarios.  Includes a graphical modeling environment.
  documentation:
  - note: The manual for SLiM itself
    type:
    - User manual
    url: http://benhaller.com/slim/SLiM_Manual.pdf
  - note: The manual for Eidos, the scripting language used by SLiM
    type:
    - User manual
    url: http://benhaller.com/slim/Eidos_Manual.pdf
  - note: Quick reference sheets for SLiM and Eidos
    type:
    - Quick start guide
    url: http://benhaller.com/slim/SLiMEidosRefSheets.zip
  download:
  - note: A source archive for the command-line `slim` tool only.  Complete source
      code is on GitHub, but most platforms have an installer anyway; see the manual,
      chapter 2, for installation instructions.
    type: Source code
    url: http://benhaller.com/slim/SLiM.zip
    version: null
  - note: The GitHub page for the current release version, to obtain full source code.
    type: Downloads page
    url: https://github.com/MesserLab/SLiM/releases/latest
    version: null
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Run individual-based eco-evolutionary simulations with explicit genetics
    operation:
    - term: DNA substitution modelling
      uri: http://edamontology.org/operation_0550
    - term: Sequence generation
      uri: http://edamontology.org/operation_0230
    - term: Ecological modelling
      uri: http://edamontology.org/operation_3946
    output: []
  homepage: https://messerlab.org/slim/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-05-05T19:54:01.119992Z'
  license: GPL-3.0
  link:
  - note: SLiM home page in the Messer Lab website
    type:
    - Software catalogue
    url: https://messerlab.org/slim/
  - note: GitHub repository for SLiM
    type:
    - Repository
    url: https://github.com/MesserLab/SLiM
  - note: Discussion forum for SLiM questions
    type:
    - Discussion forum
    url: https://groups.google.com/g/slim-discuss
  - note: Announcements mailing list
    type:
    - Mailing list
    url: https://groups.google.com/g/slim-announce
  maturity: Mature
  name: SLiM
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: bchaller
  publication:
  - doi: 10.1093/molbev/msy228
    metadata: null
    note: 'B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond
      the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.'
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1093/molbev/msy237
    metadata: null
    note: B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners.
      Molecular Biology and Evolution 36(5), 1101–1109.
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  - doi: 10.1111/1755-0998.12968
    metadata: null
    note: B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019).
      Tree-sequence recording in SLiM opens new horizons for forward-time simulation
      of whole genomes. Molecular Ecology Resources 19(2), 552–566.
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  - doi: 10.1086/723601
    metadata: null
    note: 'B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary
      modeling. The American Naturalist 201(5), E127–E139.'
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  validated: 0
  version:
  - 4.2.2
- accessibility: Open access
  additionDate: '2023-03-08T09:19:09.284884Z'
  biotoolsCURIE: biotools:odamnet
  biotoolsID: odamnet
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: morgane.terezol@univ-amu.fr
    fundrefid: null
    gridid: null
    name: Morgane Térézol
    note: null
    orcidid: https://orcid.org/0000-0002-4090-2573
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Anaïs Baudot
    note: null
    orcidid: https://orcid.org/0000-0003-0885-7933
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ozan Ozisik
    note: null
    orcidid: https://orcid.org/0000-0001-5980-8002
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A Python package to study molecular relationship between environmental
    factors and rare diseases.
  documentation:
  - note: null
    type:
    - User manual
    url: https://odamnet.readthedocs.io/en/latest/
  download: []
  editPermission:
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    type: private
  elixirCommunity:
  - Rare Diseases
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
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    input: []
    note: null
    operation:
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Protein interaction network analysis
      uri: http://edamontology.org/operation_0276
    output: []
  homepage: https://pypi.org/project/ODAMNet/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-05-02T11:58:39.872174Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/MOohTus/ODAMNet
  maturity: null
  name: ODAMNet
  operatingSystem:
  - Linux
  otherID: []
  owner: mterezol
  publication:
  - doi: 10.1016/j.softx.2024.101701
    metadata:
      abstract: 'Environmental factors are external conditions that can affect the
        health of living organisms. For a number of rare genetic diseases, an interplay
        between genetic and environmental factors is known or suspected. However,
        the studies are limited by the scarcity of patients and the difficulties in
        gathering reliable exposure information. In order to aid in fostering research
        between environmental factors and rare diseases, we propose ODAMNet, a Python
        package to investigate the possible relationships between chemicals, which
        are a subset of environmental factors, and rare diseases. ODAMNet offers three
        different and complementary bioinformatics approaches for the exploration
        of relationships: overlap analysis, active module identification and random
        walk with restart. ODAMNet allows systematic analysis of chemical - rare disease
        relationships and generation of hypotheses for further investigation of effect
        mechanisms.'
      authors:
      - name: Terezol M.
      - name: Baudot A.
      - name: Ozisik O.
      citationCount: 0
      date: '2024-05-01T00:00:00Z'
      journal: SoftwareX
      title: 'ODAMNet: A Python package to identify molecular relationships between
        chemicals and rare diseases using overlap, active module and random walk approaches'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-30T12:35:46.193814Z'
  biotoolsCURIE: biotools:jeasytfm
  biotoolsID: jeasytfm
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: philippe.carl@unistra.fr
    fundrefid: null
    gridid: null
    name: Philippe Carl
    note: null
    orcidid: https://orcid.org/0000-0001-8063-3294
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Philippe Rondé
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Open-source software package for the analysis of large 2D TFM data
    within ImageJ.
  documentation:
  - note: null
    type:
    - User manual
    url: http://questpharma.u-strasbg.fr/JEasyTFM_manual.html
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Splitting
      uri: http://edamontology.org/operation_3359
    - term: Editing
      uri: http://edamontology.org/operation_3096
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: http://questpharma.u-strasbg.fr/JEasyTFM.html
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-30T12:35:46.196223Z'
  license: null
  link: []
  maturity: null
  name: JeasyTFM
  operatingSystem: []
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/BIOADV/VBAD156
    metadata:
      abstract: 'Motivation: Cells adhering to the extracellular matrix can sense
        and respond to a wide variety of chemical and physical features of the adhesive
        surface. Traction force microscopy (TFM) allows determining the tensile forces
        exerted by the cells on their substrate with high resolution. Results: To
        allow broad access of this techniques to cell biology laboratories we developed
        JeasyTFM, an open-source ImageJ package able to process multi-color and multi-position
        time-lapse pictures thus suitable for the automatic analysis of large TFM
        data.'
      authors:
      - name: Carl P.
      - name: Ronde P.
      citationCount: 0
      date: '2023-01-01T00:00:00Z'
      journal: Bioinformatics Advances
      title: 'JEasyTFM: an open-source software package for the analysis of large
        2D TFM data within ImageJ'
    note: null
    pmcid: PMC10625472
    pmid: '37928344'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Cytometry
    uri: http://edamontology.org/topic_3934
  - term: Physics
    uri: http://edamontology.org/topic_3318
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-26T12:47:18.401889Z'
  biotoolsCURIE: biotools:hybkit
  biotoolsID: hybkit
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ds@ufl.edu
    fundrefid: null
    gridid: null
    name: Daniel Stribling
    note: null
    orcidid: https://orcid.org/0000-0002-0649-9506
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: rrenne@ufl.edu
    fundrefid: null
    gridid: null
    name: Rolf Renne
    note: null
    orcidid: https://orcid.org/0000-0001-7391-8806
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Python API and command-line toolkit for hybrid sequence data from chimeric
    RNA methods.
  documentation:
  - note: null
    type:
    - User manual
    url: http://hybkit.readthedocs.io
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: miRNA target prediction
      uri: http://edamontology.org/operation_0463
    - term: miRNA expression analysis
      uri: http://edamontology.org/operation_3792
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    output: []
  homepage: https://pypi.org/project/hybkit/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-04-26T12:47:18.404450Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: http://github.com/RenneLab/hybkit
  maturity: null
  name: Hybkit
  operatingSystem: []
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAD721
    metadata:
      abstract: 'Summary: Experimental methods using microRNA/target ligation have
        recently provided significant insights into microRNA functioning through generation
        of chimeric (hybrid) RNA sequences. Here, we introduce Hybkit, a Python3 API,
        and command-line toolkit for analysis of hybrid sequence data in the "hyb"file
        format to enable customizable evaluation and annotation of hybrid characteristics.
        The Hybkit API includes a suite of python objects for developing custom analyses
        of hybrid data as well as miRNA-specific analysis methods, built-in plotting
        of analysis results, and incorporation of predicted miRNA/target interactions
        in Vienna format.'
      authors:
      - name: Stribling D.
      - name: Gay L.A.
      - name: Renne R.
      citationCount: 0
      date: '2023-12-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Hybkit: A Python API and command-line toolkit for hybrid sequence data
        from chimeric RNA methods'
    note: null
    pmcid: PMC10701094
    pmid: '38006335'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: RNA immunoprecipitation
    uri: http://edamontology.org/topic_3794
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-04-19T10:26:21.921850Z'
  biotoolsCURIE: biotools:mcptaggr
  biotoolsID: mcptaggr
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: f.tomoyuki@okayama-u.ac.jp
    fundrefid: null
    gridid: null
    name: Tomoyuki Furuta
    note: null
    orcidid: https://orcid.org/0000-0002-0869-6626
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: R package for accurate genotype calling in reduced representation sequencing
    data by eliminating error-prone markers based on genome comparison.
  documentation:
  - note: null
    type:
    - User manual
    url: https://tomoyukif.github.io/MCPtaggR/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: Demultiplexing
      uri: http://edamontology.org/operation_3933
    - term: SNP detection
      uri: http://edamontology.org/operation_0484
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output: []
  homepage: https://github.com/tomoyukif/MCPtaggR
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-04-19T10:26:21.924007Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: MCPtaggR
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/DNARES/DSAD027
    metadata:
      abstract: Reduced representation sequencing (RRS) offers cost-effective, high-throughput
        genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are
        typically mapped onto a reference genome. However, mapping reads harbouring
        mismatches against the reference can potentially result in mismapping and
        biased mapping, leading to the detection of error-prone markers that provide
        incorrect genotype information. We established a genotype-calling pipeline
        named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate
        genotyping by eliminating error-prone markers. MCPtagg was designed for the
        RRS-based genotyping of a population derived from a biparental cross. The
        MCPtagg pipeline filters out error-prone markers prior to genotype calling
        based on marker collinearity information obtained by comparing the genome
        sequences of the parents of a population to be genotyped. A performance evaluation
        on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore,
        our performance test using a genome assembly that was obtained by genome sequence
        polishing on an available genome assembly suggests that our pipeline performs
        well with converted genomes, rather than necessitating de novo assembly. This
        demonstrates its flexibility and scalability. The R package, MCPtaggR, was
        developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR.
      authors:
      - name: Furuta T.
      - name: Yamamoto T.
      citationCount: 0
      date: '2024-02-01T00:00:00Z'
      journal: DNA Research
      title: 'MCPtaggR: R package for accurate genotype calling in reduced representation
        sequencing data by eliminating error-prone markers based on genome comparison'
    note: null
    pmcid: PMC10799318
    pmid: '38134958'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-04-19T10:01:19.463835Z'
  biotoolsCURIE: biotools:predictonco
  biotoolsID: predictonco
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jiri@chemi.muni.cz
    fundrefid: null
    gridid: null
    name: Jiri Damborsky
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: davidbednar1208@gmail.com
    fundrefid: null
    gridid: null
    name: David Bednar
    note: null
    orcidid: https://orcid.org/0000-0002-6803-0340
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: A web tool supporting decision-making in precision oncology by extending
    bioinformatics predictions with advanced computing and machine learning.
  documentation:
  - note: null
    type:
    - User manual
    url: https://loschmidt.chemi.muni.cz/predictonco/help
  download: []
  editPermission:
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    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Virtual screening
      uri: http://edamontology.org/operation_3938
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output: []
  homepage: https://loschmidt.chemi.muni.cz/predictonco
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-19T10:01:19.465909Z'
  license: null
  link: []
  maturity: null
  name: PredictONCO
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/BIB/BBAD441
    metadata:
      abstract: PredictONCO 1.0 is a unique web server that analyzes effects of mutations
        on proteins frequently altered in various cancer types. The server can assess
        the impact of mutations on the protein sequential and structural properties
        and apply a virtual screening to identify potential inhibitors that could
        be used as a highly individualized therapeutic approach, possibly based on
        the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art
        computational tools combined with information from established databases.
        The user interface was carefully designed for the target specialists in precision
        oncology, molecular pathology, clinical genetics and clinical sciences. The
        tool summarizes the effect of the mutation on protein stability and function
        and currently covers 44 common oncological targets. The binding affinities
        of Food and Drug Administration/ European Medicines Agency -approved drugs
        with the wild-type and mutant proteins are calculated to facilitate treatment
        decisions. The reliability of predictions was confirmed against 108 clinically
        validated mutations. The server provides a fast and compact output, ideal
        for the often time-sensitive decision-making process in oncology. Three use
        cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified
        in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified
        in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor
        in a patient with congenital mismatch repair deficiency highlight how the
        tool can increase levels of confidence regarding the pathogenicity of the
        variants and identify the most effective inhibitors. The server is available
        at https://loschmidt.chemi.muni.cz/predictonco.
      authors:
      - name: Stourac J.
      - name: Borko S.
      - name: Khan R.T.
      - name: Pokorna P.
      - name: Dobias A.
      - name: Planas-Iglesias J.
      - name: Mazurenko S.
      - name: Pinto G.
      - name: Szotkowska V.
      - name: Sterba J.
      - name: Slaby O.
      - name: Damborsky J.
      - name: Bednar D.
      citationCount: 0
      date: '2024-01-01T00:00:00Z'
      journal: Briefings in Bioinformatics
      title: 'PredictONCO: A web tool supporting decision-making in precision oncology
        by extending the bioinformatics predictions with advanced computing and machine
        learning'
    note: null
    pmcid: PMC10709543
    pmid: '38066711'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Personalised medicine
    uri: http://edamontology.org/topic_3577
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-04-19T08:02:22.142231Z'
  biotoolsCURIE: biotools:scipion_chem
  biotoolsID: scipion_chem
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ddelhoyo@cnb.csic.es
    fundrefid: null
    gridid: null
    name: Daniel Del Hoyo
    note: null
    orcidid: https://orcid.org/0009-0005-3321-1810
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: An open platform for virtual drug screening.
  documentation:
  - note: null
    type:
    - User manual
    url: https://scipion-chem.github.io/docs/publications/scipion-chem_vds
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Virtual screening
      uri: http://edamontology.org/operation_3938
    - term: Protein-protein docking
      uri: http://edamontology.org/operation_3899
    - term: Epitope mapping
      uri: http://edamontology.org/operation_0416
    output: []
  homepage: https://github.com/scipion-chem
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-04-19T08:02:22.144325Z'
  license: AGPL-3.0
  link: []
  maturity: null
  name: Scipion-chem
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1021/ACS.JCIM.3C01085
    metadata:
      abstract: Virtual drug screening (VDS) tackles the problem of drug discovery
        by computationally reducing the number of potential pharmacological molecules
        that need to be tested experimentally to find a new drug. To do so, several
        approaches have been developed through the years, typically focusing on either
        the physicochemical characteristics of the receptor structure (structure-based
        virtual screening) or those of the potential ligands (ligand-based virtual
        screening). Scipion is a workflow engine well suited for structural studies
        of biological macromolecules. Here, we present Scipion-chem, a new branch
        oriented to VDS. A total of 11 plugins have already been integrated from the
        most common programs used in the field. They can be used through the Scipion
        graphical user interface to execute and analyze typical VDS tasks. In addition,
        we have developed several consensus protocols that combine results from the
        different integrated programs to generate more robust predictions. Backstage,
        Scipion also facilitates the interoperability of those different software
        packages while tracking all of the intermediate files, parameters, and user
        decisions. In summary, in this article, we present Scipion-chem. This accessible,
        interoperable, and traceable platform provides the user with all of the tools
        to carry out a successful VDS workflow. Scipion-chem is openly available at
        https://github.com/scipion-chem.
      authors:
      - name: Del Hoyo D.
      - name: Salinas M.
      - name: Lomas A.
      - name: Ulzurrun E.
      - name: Campillo N.E.
      - name: Sorzano C.O.
      citationCount: 0
      date: '2023-12-25T00:00:00Z'
      journal: Journal of Chemical Information and Modeling
      title: 'Scipion-Chem: An Open Platform for Virtual Drug Screening'
    note: null
    pmcid: PMC10751785
    pmid: '38052452'
    type: []
    version: null
  relation: []
  toolType:
  - Plug-in
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Pharmacology
    uri: http://edamontology.org/topic_0202
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-04-19T07:46:31.537317Z'
  biotoolsCURIE: biotools:tcgaplot
  biotoolsID: tcgaplot
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: wangxiong@tjh.tjmu.edu.cn
    fundrefid: null
    gridid: null
    name: Xiong Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: An R package for integrative pan-cancer analysis and visualization
    of TCGA multi-omics data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/tjhwangxiong/TCGAplot/blob/main/vignettes/TCGAplot.Rmd
  - note: null
    type:
    - User manual
    url: https://github.com/tjhwangxiong/TCGAplot/blob/main/vignettes/TCGAplot
  download:
  - note: null
    type: Software package
    url: https://github.com/tjhwangxiong/TCGAplot/releases/download/v4.0.0/TCGAplot_4.0.0.zip
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Expression correlation analysis
      uri: http://edamontology.org/operation_3463
    - term: Dot plot plotting
      uri: http://edamontology.org/operation_0490
    output: []
  homepage: https://github.com/tjhwangxiong/TCGAplot
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-04-19T07:46:50.933786Z'
  license: MIT
  link: []
  maturity: null
  name: TCGAplot
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/S12859-023-05615-3
    metadata:
      abstract: 'Background: Pan-cancer analysis examines both the commonalities and
        heterogeneity among genomic and cellular alterations across numerous types
        of tumors. Pan-cancer analysis of gene expression, tumor mutational burden
        (TMB), microsatellite instability (MSI), and tumor immune microenvironment
        (TIME), and methylation becomes available based on the multi-omics data from
        The Cancer Genome Atlas Program (TCGA). Some online tools provide analysis
        of gene and protein expression, mutation, methylation, and survival for TCGA
        data. However, these online tools were either Uni-functional or were not able
        to perform analysis of user-defined functions. Therefore, we created the TCGAplot
        R package to facilitate perform pan-cancer analysis and visualization of the
        built-in multi-omic TCGA data. Results: TCGAplot provides several functions
        to perform pan-cancer paired/unpaired differential gene expression analysis,
        pan-cancer correlation analysis between gene expression and TMB, MSI, TIME,
        and promoter methylation. Functions for visualization include paired/unpaired
        boxplot, survival plot, ROC curve, heatmap, scatter, radar chart, and forest
        plot. Moreover, gene set based pan-cancer and tumor specific analyses were
        also available. Finally, all these built-in multi-omic data could be extracted
        for implementation for user-defined functions, making the pan-cancer analysis
        much more convenient.\ Conclusions: We developed an R-package for integrative
        pan-cancer analysis and visualization of TCGA multi-omics data. The source
        code and pre-built package are available at GitHub (https://github.com/tjhwangxiong/TCGAplot).'
      authors:
      - name: Liao C.
      - name: Wang X.
      citationCount: 2
      date: '2023-12-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'TCGAplot: an R package for integrative pan-cancer analysis and visualization
        of TCGA multi-omics data'
    note: null
    pmcid: PMC10726608
    pmid: '38105215'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: null
  additionDate: '2024-02-02T14:42:46.030561Z'
  biotoolsCURIE: biotools:hictk
  biotoolsID: hictk
  collectionID: []
  community: null
  confidence_flag: null
  cost: null
  credit: []
  description: Blazing fast toolkit to work with .hic and .cool files
  documentation:
  - note: null
    type:
    - User manual
    url: https://hictk.readthedocs.io/en/latest/index.html
  download:
  - note: null
    type: Downloads page
    url: https://github.com/paulsengroup/hictk/releases
    version: null
  - note: null
    type: Binaries
    url: https://anaconda.org/bioconda/hictk
    version: null
  - note: null
    type: Container file
    url: https://github.com/paulsengroup/hictk/pkgs/container/hictk
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/paulsengroup/hictk
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-18T08:55:19.020424Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/paulsengroup/hictk
  - note: null
    type:
    - Issue tracker
    url: https://github.com/paulsengroup/hictk/issues
  maturity: null
  name: hictk
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: robomics
  publication:
  - doi: 10.1101/2023.11.26.568707
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: hictkpy
    type: usedBy
  - biotoolsID: hictkr
    type: usedBy
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.0.1
  - 0.0.2
  - 0.0.3
  - 0.0.4
  - 0.0.5
  - 0.0.6
  - 0.0.7
  - 0.0.8
  - 0.0.9
  - 0.0.10
  - 0.0.11
  - 0.0.12
- accessibility: Open access
  additionDate: '2024-04-16T14:10:00.623929Z'
  biotoolsCURIE: biotools:oggmap
  biotoolsID: oggmap
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ullrich@evolbio.mpg.de
    fundrefid: null
    gridid: null
    name: Kristian K Ullrich
    note: null
    orcidid: https://orcid.org/0000-0003-4308-9626
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nikoleta E Glytnasi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Python package to extract gene ages per orthogroup and link them with
    single-cell RNA data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://oggmap.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Dimensionality reduction
      uri: http://edamontology.org/operation_3935
    output: []
  homepage: https://github.com/kullrich/oggmap
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-04-16T14:10:00.646441Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: oggmap
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAD657
    metadata:
      abstract: 'Summary: For model species, single-cell RNA-based cell atlases are
        available. A good cell atlas includes all major stages in a species’ ontogeny,
        and soon, they will be standard even for nonmodel species. Here, we propose
        a Python package called oggmap, which allows for the easy extraction of an
        orthomap (gene ages per orthogroup) for any given query species from OrthoFinder
        and other gene family data resources, like homologous groups from eggNOG or
        PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic
        species which can be further used to calculate gene age-weighted expression
        data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited
        to one transcriptome evolutionary index, oggmap can visualize the individual
        gene category (e.g. age class, nucleotide diversity bin) and their corresponding
        expression profiles to investigate scRNA-based cell type assignments in an
        evolutionary context.'
      authors:
      - name: Ullrich K.K.
      - name: Glytnasi N.E.
      citationCount: 1
      date: '2023-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'oggmap: a Python package to extract gene ages per orthogroup and link
        them with single-cell RNA data'
    note: null
    pmcid: PMC10663984
    pmid: '37952198'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  validated: 0
  version: []
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