count: 29605
list:
- accessibility: Open access
  additionDate: '2024-04-30T12:08:01.090084Z'
  biotoolsCURIE: biotools:scan_db
  biotoolsID: scan_db
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: zhanglm36@mail.sysu.edu.cn
    fundrefid: null
    gridid: null
    name: Liangming Zhang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: ronglm@mail.sysu.edu.cn
    fundrefid: null
    gridid: null
    name: Limin Rong
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: xdwang@fuccb.com
    fundrefid: null
    gridid: null
    name: Xiangdong Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Dongsheng Chen
    note: null
    orcidid: https://orcid.org/0000-0002-7196-4136
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: SCAN is a neural database that combines single cell transcriptome and
    spatial transcriptome data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Neurite measurement
      uri: http://edamontology.org/operation_3450
    output: []
  homepage: http://scanatlas.net
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-30T12:08:01.092348Z'
  license: null
  link: []
  maturity: null
  name: SCAN
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/NAR/GKAD895
    metadata:
      abstract: The nervous system is one of the most complicated and enigmatic systems
        within the animal kingdom. Recently, the emergence and development of spatial
        transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq) technologies
        have provided an unprecedented ability to systematically decipher the cellular
        heterogeneity and spatial locations of the nervous system from multiple unbiased
        aspects. However, efficiently integrating, presenting and analyzing massive
        multiomic data remains a huge challenge. Here, we manually collected and comprehensively
        analyzed high-quality scRNA-seq and ST data from the nervous system, covering
        10 679 684 cells. In addition, multi-omic datasets from more than 900 species
        were included for extensive data mining from an evolutionary perspective.
        Furthermore, over 100 neurological diseases (e.g. Alzheimer’s disease, Parkinson’s
        disease, Down syndrome) were systematically analyzed for high-throughput screening
        of putative biomarkers. Differential expression patterns across developmental
        time points, cell types and ST spots were discerned and subsequently subjected
        to extensive interpretation. To provide researchers with efficient data exploration,
        we created a new database with interactive interfaces and integrated functions
        called the Spatiotemporal Cloud Atlas for Neural cells (SCAN), freely accessible
        at http://47.98.139.124:8799 or http://scanatlas.net. SCAN will benefit the
        neuroscience research community to better exploit the spatiotemporal atlas
        of the neural system and promote the development of diagnostic strategies
        for various neurological disorders.
      authors:
      - name: Deng Y.
      - name: Lu Y.
      - name: Li M.
      - name: Shen J.
      - name: Qin S.
      - name: Zhang W.
      - name: Zhang Q.
      - name: Shen Z.
      - name: Li C.
      - name: Jia T.
      - name: Chen P.
      - name: Peng L.
      - name: Chen Y.
      - name: Zhang W.
      - name: Liu H.
      - name: Zhang L.
      - name: Rong L.
      - name: Wang X.
      - name: Chen D.
      citationCount: 0
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'SCAN: Spatiotemporal Cloud Atlas for Neural cells'
    note: null
    pmcid: PMC10767991
    pmid: '37930842'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Neurobiology
    uri: http://edamontology.org/topic_3304
  - term: Neurology
    uri: http://edamontology.org/topic_3334
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-30T08:41:07.253380Z'
  biotoolsCURIE: biotools:lncpcd
  biotoolsID: lncpcd
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ningsw@ems.hrbmu.edu.cn
    fundrefid: null
    gridid: null
    name: Shangwei Ning
    note: null
    orcidid: https://orcid.org/0000-0003-4079-8945
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: wangjian_427@163.com
    fundrefid: null
    gridid: null
    name: Lihua Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: wanglh211@163.com
    fundrefid: null
    gridid: null
    name: Jianjian Wang
    note: null
    orcidid: https://orcid.org/0000-0001-5568-4612
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Manually curated database of experimentally supported associations
    between lncRNA-mediated programmed cell death and diseases.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    output: []
  homepage: http://spare4.hospital.studio:9000/lncPCD/Home.jsp
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-30T08:41:07.255470Z'
  license: null
  link: []
  maturity: null
  name: LncPCD
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/DATABASE/BAAD087
    metadata:
      abstract: 'Programmed cell death (PCD) refers to controlled cell death that
        is conducted to keep the internal environment stable. Long noncoding RNAs
        (lncRNAs) participate in the progression of PCD in a variety of diseases.
        However, no specialized online repository is available to collect and store
        the associations between lncRNA-mediated PCD and diseases. Here, we developed
        LncPCD, a comprehensive database that provides information on experimentally
        supported associations of lncRNA-mediated PCD with diseases. The current version
        of LncPCD documents 6666 associations between five common types of PCD (apoptosis,
        autophagy, ferroptosis, necroptosis and pyroptosis) and 1222 lncRNAs in 331
        diseases.We also manually curated a wealth of information: (1) 7 important
        lncRNA regulatory mechanisms, (2) 310 PCD-associated cell types in three species,
        (3) detailed information on lncRNA subcellular locations and (4) clinical
        applications for lncRNA-mediated PCD in diseases. Additionally, 10 single-cell
        sequencing datasets were integrated into LncPCD to characterize the dynamics
        of lncRNAs in diseases. Overall, LncPCD is an extremely useful resource for
        understanding the functions and mechanisms of lncRNA-mediated PCD in diseases.'
      authors:
      - name: He N.
      - name: Li D.
      - name: Xu F.
      - name: Jin J.
      - name: Li L.
      - name: Tian L.
      - name: Chen B.
      - name: Li X.
      - name: Ning S.
      - name: Wang L.
      - name: Wang J.
      citationCount: 0
      date: '2023-01-01T00:00:00Z'
      journal: Database
      title: 'LncPCD: a manually curated database of experimentally supported associations
        between lncRNA-mediated programmed cell death and diseases'
    note: null
    pmcid: PMC10681436
    pmid: '38011720'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Cardiology
    uri: http://edamontology.org/topic_3335
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-30T08:15:41.767832Z'
  biotoolsCURIE: biotools:atlas_db
  biotoolsID: atlas_db
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jean-christophe.gelly@u-paris.fr
    fundrefid: null
    gridid: null
    name: Jean-Christophe Gelly
    note: null
    orcidid: https://orcid.org/0000-0001-5138-361X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: tatiana.galochkina@u-paris.fr
    fundrefid: null
    gridid: null
    name: Tatiana Galochkina
    note: null
    orcidid: https://orcid.org/0000-0002-3608-5208
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: ATLAS gathers standardized molecular dynamics simulations of protein
    structures accompanied by their analysis in the form of interactive diagrams and
    trajectory visualisation.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Simulation analysis
      uri: http://edamontology.org/operation_0244
    - term: Trajectory visualization
      uri: http://edamontology.org/operation_3890
    - term: Protein-protein docking
      uri: http://edamontology.org/operation_3899
    - term: Protein geometry calculation
      uri: http://edamontology.org/operation_0249
    output: []
  homepage: https://www.dsimb.inserm.fr/ATLAS
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-30T08:15:41.770796Z'
  license: null
  link: []
  maturity: null
  name: ATLAS
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/NAR/GKAD1084
    metadata:
      abstract: Dynamical behaviour is one of the most crucial protein characteristics.
        Despite theãdvances in the field of protein str uct ure resolutionãnd predic-
        tion,ãnalysisãnd prediction of protein dynamic properties remainsã major challenge,
        mostly due to the lowãccessibility of dataãnd its diversityãnd heterogeneity.
        Toãddress this issue, we present ATLA S ,ã database of standardisedãll-atom
        molecular dynamics simulations,ãccompanied by theirãnalysis in the form of
        interactive diagramsãnd trajectory visualisation. ATLAS offersã large-scale
        viewãnd valuable insights on protein dynamics forã largeãnd representative
        set of proteins, by combining data obtained through molecular dynamics simulations
        with information e xtracted from e xperimental str uct ures. Users can easilyãnalyse
        dynamic properties of functional protein regions, suchãs domain limits (hinge
        positions)ãnd residues in v olv ed in interaction with other biological molecules.
        Additionally, the database enables exploration of proteins with uncommon dynamic
        properties conditioned by their environment suchãs chameleon subsequencesãnd
        Dual Personality Fragments. The ATLAS database is freelyã vãilableãt https://
        www.dsimb.inserm.fr/ ATLAS .
      authors:
      - name: Meersche Y.V.
      - name: Cretin G.
      - name: Gheeraert A.
      - name: Gelly J.-C.
      - name: Galochkina T.
      citationCount: 3
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'ATLA S: prot ein flexibility description fromãtomistic molecular dynamics
        simulations'
    note: null
    pmcid: PMC10767941
    pmid: '37986215'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Protein folding, stability and design
    uri: http://edamontology.org/topic_0130
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-08-29T11:42:48.137925Z'
  biotoolsCURIE: biotools:biotools-linter
  biotoolsID: biotools-linter
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: 251814@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Filip Rusz
    note: null
    orcidid: https://orcid.org/0009-0002-0046-9725
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: A rule-based checker for the bio.tools database.
  documentation:
  - note: null
    type:
    - General
    url: https://biotools-linter.biodata.ceitec.cz/docs
  - note: null
    type:
    - API documentation
    url: https://biotools-linter.biodata.ceitec.cz/api/documentation/
  download:
  - note: null
    type: Source code
    url: https://github.com/3top1a/biotools-linter
    version: null
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: --lint
    input: []
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output: []
  homepage: https://biotools-linter.biodata.ceitec.cz/
  homepage_status: 0
  language:
  - Python
  - Other
  lastUpdate: '2024-04-27T14:02:11.136488Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/3top1a/biotools-linter
  - note: null
    type:
    - Technical monitoring
    url: https://biotools-linter.biodata.ceitec.cz/dash/
  maturity: Emerging
  name: biotools-linter
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: FilipRusz
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Web service
  - Web API
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-26T13:01:05.133566Z'
  biotoolsCURIE: biotools:ncrnadrug
  biotoolsID: ncrnadrug
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: guoanyuan@wchscu.cn
    fundrefid: null
    gridid: null
    name: An-Yuan Guo
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: weijiang@nuaa.edu.cn
    fundrefid: null
    gridid: null
    name: Wei Jiang
    note: null
    orcidid: https://orcid.org/0000-0003-1591-4721
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Database for validated and predicted ncRNAs associated with drug resistance
    and targeted by drugs.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: miRNA target prediction
      uri: http://edamontology.org/operation_0463
    - term: miRNA expression analysis
      uri: http://edamontology.org/operation_3792
    output: []
  homepage: http://www.jianglab.cn/ncRNADrug
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-26T13:01:05.135924Z'
  license: null
  link: []
  maturity: null
  name: ncRNADrug
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/NAR/GKAD1042
    metadata:
      abstract: Drug resistance isã major barrier in cancer treatmentãndãnticancer
        drug de v elopment. Gro wing e vidence indicates that non-coding RNAs (ncR-
        NA s), especially microRNA s (miRNA s), long non-coding RNA s (lncRNA s)ãnd
        circular RNA s (circRNA s), pla y piv otal roles in cancer progression, therapy,ãnd
        drug resistance. Furthermore, ncRNAs ha v e been pro v en to be promising
        no v el therapeutic targets f or cancer treatment. R e v ers- ing dysregulated
        ncRNAs by drugs holds significant potentialãsãn effective therapeutic strategy
        for overcoming drug resistance. Therefore, w e de v eloped ncRNADrug,ãn integratedãnd
        comprehensive resource that records manually curatedãnd computationally predicted
        ncRNAsãssociated with drug resistance, ncRNAs targeted by drugs,ãs wellãs
        potential drug combinations for the treatment of resistant cancer. Cur- rently,
        ncRNADrug collects 29 551 experimentally validated entries involving 9195
        ncRNAs (2248 miRNAs, 4145 lncRNAsãnd 2802 circRNAs)ãssociated with the drug
        resistance of 266 drugs,ãnd 32 969 entries in v olving 10 480 ncRNAs (4338
        miRNAs, 6087 lncRNAsãnd 55 circRNAs) targeted by 965 drugs. Inãddition, ncRNADrugãlso
        containsãssociations between ncRNAsãnd drugs predicted from ncRNA expression
        profiles by differential expressionãnalysis. Altogether, ncRNADrug surpasses
        the existing related databases in both data volumeãnd functionality. It will
        beã useful resource for drug developmentãnd cancer treatment. ncRNADrug isãvailableãt
        http:// www.jianglab.cn/ ncRNADrug .
      authors:
      - name: Cao X.
      - name: Zhou X.
      - name: Hou F.
      - name: Huang Y.-E.
      - name: Yuan M.
      - name: Long M.
      - name: Chen S.
      - name: Lei W.
      - name: Zhu J.
      - name: Chen J.
      - name: Zhang T.
      - name: Guo A.-Y.
      - name: Jiang W.
      citationCount: 1
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: ncRNADrug:ã database for validatedãnd predicted ncRNAsãssociated with
        drug resistanceãnd targeted by drugs
    note: null
    pmcid: PMC10767907
    pmid: '37953323'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Drug development
    uri: http://edamontology.org/topic_3373
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-26T12:51:51.787252Z'
  biotoolsCURIE: biotools:g-aligner
  biotoolsID: g-aligner
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: yu_lab@sdfmu.edu.cn
    fundrefid: null
    gridid: null
    name: Changbin Yu
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ruimin Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Graph-based feature alignment method for untargeted LC-MS-based metabolomics.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Feature extraction
      uri: http://edamontology.org/operation_3937
    - term: Sequence alignment validation
      uri: http://edamontology.org/operation_0447
    - term: Retention time prediction
      uri: http://edamontology.org/operation_3633
    output: []
  homepage: https://github.com/CSi-Studio/G-Aligner
  homepage_status: 0
  language:
  - Python
  - Java
  lastUpdate: '2024-04-26T12:51:51.789259Z'
  license: null
  link: []
  maturity: null
  name: G-Aligner
  operatingSystem: []
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/S12859-023-05525-4
    metadata:
      abstract: 'Background: Liquid chromatography–mass spectrometry is widely used
        in untargeted metabolomics for composition profiling. In multi-run analysis
        scenarios, features of each run are aligned into consensus features by feature
        alignment algorithms to observe the intensity variations across runs. However,
        most of the existing feature alignment methods focus more on accurate retention
        time correction, while underestimating the importance of feature matching.
        None of the existing methods can comprehensively consider feature correspondences
        among all runs and achieve optimal matching. Results: To comprehensively analyze
        feature correspondences among runs, we propose G-Aligner, a graph-based feature
        alignment method for untargeted LC–MS data. In the feature matching stage,
        G-Aligner treats features and potential correspondences as nodes and edges
        in a multipartite graph, considers the multi-run feature matching problem
        an unbalanced multidimensional assignment problem, and provides three combinatorial
        optimization algorithms to find optimal matching solutions. In comparison
        with the feature alignment methods in OpenMS, MZmine2 and XCMS on three public
        metabolomics benchmark datasets, G-Aligner achieved the best feature alignment
        performance on all the three datasets with up to 9.8% and 26.6% increase in
        accurately aligned features and analytes, and helped all comparison software
        obtain more accurate results on their self-extracted features by integrating
        G-Aligner to their analysis workflow. G-Aligner is open-source and freely
        available at https://github.com/CSi-Studio/G-Aligner under a permissive license.
        Benchmark datasets, manual annotation results, evaluation methods and results
        are available at https://doi.org/10.5281/zenodo.8313034 Conclusions: In this
        study, we proposed G-Aligner to improve feature matching accuracy for untargeted
        metabolomics LC–MS data. G-Aligner comprehensively considered potential feature
        correspondences between all runs, converting the feature matching problem
        as a multidimensional assignment problem (MAP). In evaluations on three public
        metabolomics benchmark datasets, G-Aligner achieved the highest alignment
        accuracy on manual annotated and popular software extracted features, proving
        the effectiveness and robustness of the algorithm.'
      authors:
      - name: Wang R.
      - name: Lu M.
      - name: An S.
      - name: Wang J.
      - name: Yu C.
      citationCount: 0
      date: '2023-12-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'G-Aligner: a graph-based feature alignment method for untargeted LC–MS-based
        metabolomics'
    note: null
    pmcid: PMC10644574
    pmid: '37964228'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-26T12:49:02.139884Z'
  biotoolsCURIE: biotools:rvdb
  biotoolsID: rvdb
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Bo Liu
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: zhangting@ipbcams.ac.cn
    fundrefid: null
    gridid: null
    name: Ting Zhang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Fan Yang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: A comprehensive rhinovirus database and analysis platform integrating
    many online analysis functions.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    - term: Phylogenetic inference
      uri: http://edamontology.org/operation_0323
    - term: Database search
      uri: http://edamontology.org/operation_2421
    output: []
  homepage: http://rvdb.mgc.ac.cn
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-26T12:49:02.142203Z'
  license: null
  link: []
  maturity: null
  name: RVdb
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/NAR/GKAD937
    metadata:
      abstract: Rhinovirus (RV), a prominent causative agent of both upper and lower
        respiratory diseases, ranks among the most prevalent human respiratory viruses.
        RV infections are associated with various illnesses, including colds, asthma
        exacerbations, croup and pneumonia, imposing significant and extended societal
        burdens. Characterized by a high mutation rate and genomic diversity, RV displays
        a diverse serological landscape, encompassing a total of 174 serotypes identified
        to date. Understanding RV genetic diversity is crucial for epidemiological
        surveillance and investigation of respiratory diseases. This study introduces
        a comprehensive and high-quality RV data resource, designated RVdb (http://rvdb.mgc.ac.cn),
        covering 26 909 currently identified RV strains, along with RV-related sequences,
        3D protein structures and publications. Furthermore, this resource features
        a suite of web-based utilities optimized for easy browsing and searching,
        as well as automatic sequence annotation, multiple sequence alignment (MSA),
        phylogenetic tree construction, RVdb BLAST and a serotyping pipeline. Equipped
        with a user-friendly interface and integrated online bioinformatics tools,
        RVdb provides a convenient and powerful platform on which to analyse the genetic
        characteristics of RVs. Additionally, RVdb also supports the efforts of virologists
        and epidemiologists to monitor and trace both existing and emerging RV-related
        infectious conditions in a public health context.
      authors:
      - name: Zhao P.
      - name: Zhou S.
      - name: Xu P.
      - name: Su H.
      - name: Han Y.
      - name: Dong J.
      - name: Sui H.
      - name: Li X.
      - name: Hu Y.
      - name: Wu Z.
      - name: Liu B.
      - name: Zhang T.
      - name: Yang F.
      citationCount: 1
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'RVdb: a comprehensive resource and analysis platform for rhinovirus
        research'
    note: null
    pmcid: PMC10768139
    pmid: '37930838'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  - Web application
  topic:
  - term: Public health and epidemiology
    uri: http://edamontology.org/topic_3305
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Respiratory medicine
    uri: http://edamontology.org/topic_3322
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  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: Open access
  additionDate: '2024-04-26T12:37:30.753656Z'
  biotoolsCURIE: biotools:phagescope
  biotoolsID: phagescope
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jianwang@cityu.edu.hk
    fundrefid: null
    gridid: null
    name: Jianping Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: shuaicli@cityu.edu.hk
    fundrefid: null
    gridid: null
    name: Shuai Cheng Li
    note: null
    orcidid: https://orcid.org/0000-0001-6246-6349
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Annotated bacteriophage database with automatic analyses and visualizations.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://phagescope.deepomics.org
  homepage_status: 0
  language: []
  lastUpdate: '2024-04-26T12:37:30.755896Z'
  license: null
  link: []
  maturity: null
  name: PhageScope
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/NAR/GKAD979
    metadata:
      abstract: Bacteriophages are viruses that infect bacteria or archaea. Understanding
        the diverse and intricate genomic architectures of phages is essential to
        study microbial ecosystems and develop phage therapy strategies. However,
        the existing phage databases are short of meticulous annotations. To this
        end, we propose PhageScope (https://phagescope.deepomics.org), an online phage
        database with comprehensive annotations. PhageScope harbors a collection of
        873 718 phage sequences from various sources. Applying fifteen state-of-the-art
        tools to perform systematic annotations and analyses, PhageScope provides
        annotations on genome completeness, host range, lifestyle information, taxonomy
        classification, nine types of structural and functional genetic elements,
        and three types of comparative genomic studies for curated phages. Additionally,
        PhageScope incorporates automatic analyses and visualizations for curated
        and customized phages, serving as an efficient platform for phage study.
      authors:
      - name: Wang R.H.
      - name: Yang S.
      - name: Liu Z.
      - name: Zhang Y.
      - name: Wang X.
      - name: Xu Z.
      - name: Wang J.
      - name: Li S.C.
      citationCount: 1
      date: '2024-01-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'PhageScope: a well-annotated bacteriophage database with automatic analyses
        and visualizations'
    note: null
    pmcid: PMC10767790
    pmid: '37904614'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Mobile genetic elements
    uri: http://edamontology.org/topic_0798
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-04-26T11:53:20.839995Z'
  biotoolsCURIE: biotools:parazitcub
  biotoolsID: parazitcub
  collectionID: []
  community: null
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: Amreahmed@psas.bsu.edu.eg
    fundrefid: null
    gridid: null
    name: Amr E. Ahmed
    note: null
    orcidid: https://orcid.org/0000-0003-0628-4422
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ali Mostafa Anwar
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: An R package to streamline the process of investigating the adaptations
    of parasites' codon usage bias.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Codon usage bias calculation
      uri: http://edamontology.org/operation_2962
    - term: Codon usage table generation
      uri: http://edamontology.org/operation_0284
    - term: Codon usage table comparison
      uri: http://edamontology.org/operation_0285
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    output: []
  homepage: https://github.com/AliYoussef96/parazitCUB
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-04-26T11:53:20.841976Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: parazitCUB
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.12688/f1000research.143223.1
    metadata:
      abstract: 'Examining the intricate association between parasites and their hosts,
        particularly at the codon level, assumes paramount importance in comprehending
        evolutionary processes and forecasting the characteristics of novel parasites.
        While diverse metrics and statistical analyses are available to explore codon
        usage bias (CUB), there presently exists no dedicated tool for examining the
        co-adaptation of codon usage between parasites and hosts. Therefore, we introduce
        the parazitCUB R package to address this challenge in a scalable and efficient
        manner, as it is capable of handling extensive datasets and simultaneously
        analyzing of multiple parasites with optimized performance. parazitCUB enables
        the elucidation of parasite-host interactions and the evolutionary patterns
        of parasites through the implementation of various indices, cluster analysis,
        multivariate analysis, and data visualization techniques. The tool can be
        accessed at the following location: https://github.com/AliYoussef96/parazitCUB'
      authors:
      - name: Anwar A.M.
      - name: Bayoumi S.
      - name: Elzalabany S.
      - name: Magdeldin S.
      - name: Ahmed A.E.
      citationCount: 0
      date: '2023-01-01T00:00:00Z'
      journal: F1000Research
      title: 'parazitCUB: An R package to streamline the process of investigating
        the adaptations of parasites'' codon usage bias'
    note: null
    pmcid: PMC10682597
    pmid: '38021405'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Parasitology
    uri: http://edamontology.org/topic_3302
  - term: Molecular evolution
    uri: http://edamontology.org/topic_3945
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  validated: 0
  version: []
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