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{ "count": 242, "next": "?page=2", "previous": null, "list": [ { "name": "ProtVar", "description": "ProtVar helps users to contextualise and evaluate human missense variation at a per-residue level. It can be accessed via genomic coordinates, IDs or protein positions in over 92% of human proteins. 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"term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2187", "term": "UniProt-like (text)" } ] } ], "note": "ProtVar maps missense variants from genomic coordinates to UniProt protein positions in all isoforms.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3661", "term": "SNP annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3779", "term": "Annotated text" }, "format": [ { "uri": "http://edamontology.org/format_2187", "term": "UniProt-like (text)" } ] } ], "note": "ProtVar annotates missense variant positions with functional and structural information for the amino acid affected, the protein region and the overall protein role from curated and high throughput sources.", "cmd": null } ], "toolType": [ "Web application", "Web API", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_2533", "term": "DNA mutation" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": null, "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://twitter.com/EBIProtVar", "type": [ "Social 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"Provider" ], "note": null }, { "name": "Prabhat Totoo", "email": null, "url": "https://www.ebi.ac.uk/people/person/prabhat-totoo/", "orcidid": "https://orcid.org/0000-0001-5923-4467", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Open Targets", "email": null, "url": "https://www.opentargets.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "community": null, "owner": "JStephenson", "additionDate": "2023-09-21T09:05:33.125111Z", "lastUpdate": "2023-09-25T09:31:39.599149Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Oligogenic resource for variant analysis (ORVAL)", "description": "ORVAL is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction, further external annotations and interactive and exploratory visualisation techniques.", "homepage": "https://orval.ibsquare.be", "biotoolsID": "Oligogenic_resource_for_variant_analysis", "biotoolsCURIE": "biotools:Oligogenic_resource_for_variant_analysis", "version": [ "3.0.0" ], "otherID": [], "relation": [ { "biotoolsID": "variant_combinaton_pathogenicity_predictor", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" }, { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "ELIXIR-BE", "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Belgium" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "https://orval.ibsquare.be/documentation", "type": [ "User manual", "FAQ" ], "note": null }, { "url": "https://orval-dev.ibsquare.be/updates", "type": [ "Release notes" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkz437", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations", "abstract": "A tremendous amount of DNA sequencing data is being produced around the world with the ambition to capture in more detail the mechanisms underlying human diseases. While numerous bioinformatics tools exist that allow the discovery of causal variants in Mendelian diseases, little to no support is provided to do the same for variant combinations, an essential task for the discovery of the causes of oligogenic diseases. ORVAL (the Oligogenic Resource for Variant AnaLysis), which is presented here, provides an answer to this problem by focusing on generating networks of candidate pathogenic variant combinations in gene pairs, as opposed to isolated variants in unique genes. This online platform integrates innovative machine learning methods for combinatorial variant pathogenicity prediction with visualization techniques, offering several interactive and exploratory tools, such as pathogenic gene and protein interaction networks, a ranking of pathogenic gene pairs, as well as visual mappings of the cellular location and pathway information. ORVAL is the first web-based exploration platform dedicated to identifying networks of candidate pathogenic variant combinations with the sole ambition to help in uncovering oligogenic causes for patients that cannot rely on the classical disease analysis tools. ORVAL is available at https://orval.ibsquare.be.", "date": "2019-07-01T00:00:00Z", "citationCount": 32, "authors": [ { "name": "Renaux A." }, { "name": "Papadimitriou S." }, { "name": "Versbraegen N." }, { "name": "Nachtegael C." }, { "name": "Boutry S." }, { "name": "Nowe A." }, { "name": "Smits G." }, { "name": "Lenaerts T." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Tom Lenaerts", "email": "tlenaert@ulb.ac.be", "url": "https://www.ibsquare.be", "orcidid": "https://orcid.org/0000-0003-3645-1455", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Alexandre Renaux", "email": "alexandre.renaux@ulb.ac.be", "url": "https://www.ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Interuniversity Institute of Bioinformatics in Brussels", "email": null, "url": "https://www.ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "tlenaert@ulb.ac.be", "additionDate": "2019-07-03T15:25:53Z", "lastUpdate": "2023-07-31T12:18:44.485919Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "emmaver" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Digenic Diseases Database (DIDA)", "description": "Digenic Diseases Database (DiDA) provides detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.", "homepage": "http://dida.ibsquare.be", "biotoolsID": "dida", "biotoolsCURIE": "biotools:dida", "version": [], "otherID": [], "relation": [ { "biotoolsID": "olida", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3661", "term": "SNP annotation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-NC-4.0", "collectionID": [ "ELIXIR-BE", "RD-Connect", "Rare Disease" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Belgium" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "http://dida.ibsquare.be/help/", "type": [ "General" ], "note": null }, { "url": "http://dida.ibsquare.be/documentation/", "type": [ "General" ], "note": "More detailed documentation." } ], "publication": [ { "doi": "10.1093/nar/gkv1068", "pmid": "26481352", "pmcid": "PMC4702791", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DIDA: A curated and annotated digenic diseases database", "abstract": "DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database is accessible via http://dida.ibsquare.be and currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided. Creating this new repository was essential as current databases do not allow one to retrieve detailed records regarding digenic combinations. Genes, variants, diseases and digenic combinations in DIDA are annotated with manually curated information and information mined from other online resources. Next to providing a unique resource for the development of new analysis methods, DIDA gives clinical and molecular geneticists a tool to find the most comprehensive information on the digenic nature of their diseases of interest.", "date": "2016-01-01T00:00:00Z", "citationCount": 69, "authors": [ { "name": "Gazzo A.M." }, { "name": "Daneels D." }, { "name": "Cilia E." }, { "name": "Bonduelle M." }, { "name": "Abramowicz M." }, { "name": "Van Dooren S." }, { "name": "Smits G." }, { "name": "Lenaerts T." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Interuniversity Institute of Bioinformatics in Brussels", "email": null, "url": "https://www.ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Tom Lenaerts", "email": "tlenaert@ulb.ac.be", "url": "http://www.ibsquare.be", "orcidid": "https://orcid.org/0000-0003-3645-1455", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Charlotte Nachtegael", "email": "Charlotte.Nachtegael@ulb.ac.be", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null } ], "community": null, "owner": "tlenaert@ulb.ac.be", "additionDate": "2016-06-24T14:08:44Z", "lastUpdate": "2023-07-31T12:04:32.220730Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "emmaver" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Variant Combination Pathogenicity Predictor (VarCoPP) 2.0", "description": "VarCoPP is a machine learning method that predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in OLIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP2.0 is a Balanced Random Forest predictor consisting of 400 decision trees. \nA variant combination can be either predicted as disease-causing (i.e. candidate or probably pathogenic) or neutral (i.e. probably neutral). \n\nVarCoPP can be applied for Single Nucleotide Variants (SNVs) and small insertions/deletions from a single individual. It is highly recommended to perform beforehand an initial variant filtering procedure and generally restrict the analysis to variants from up to 150 genes. \n\nVarCoPP was developed in the Interuniversity Institute of Bioinformatics in Brussels, under the collaboration of Université libre de Bruxelles and Vrije Universiteit Brussel.\n\nYou can use it through the online tool ORVAL: https://orval.ibsquare.be.", "homepage": "http://varcopp.ibsquare.be", "biotoolsID": "Variant_Combinaton_Pathogenicity_Predictor", "biotoolsCURIE": "biotools:Variant_Combinaton_Pathogenicity_Predictor", "version": [ "1.0", "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "oligogenic_resource_for_variant_analysis", "type": "includedIn" }, { "biotoolsID": "olida", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-BE", "RD-Connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Belgium" ], "elixirCommunity": [ "Rare Diseases" ], "link": [ { "url": "https://github.com/oligogenic/VarCoPP2.0", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/sofiapapad90/VarCoPP/", "type": [ "Repository" ], "note": null }, { "url": "https://orval.ibsquare.be", "type": [ "Service" ], "note": "Web app integrating VarCoPP2.0" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1073/pnas.1815601116", "pmid": null, "pmcid": null, "type": [], "version": "1.0", "note": null, "metadata": { "title": "Predicting disease-causing variant combinations", "abstract": "Notwithstanding important advances in the context of single-variant pathogenicity identification, novel breakthroughs in discerning the origins of many rare diseases require methods able to identify more complex genetic models. We present here the Variant Combinations Pathogenicity Predictor (VarCoPP), a machine-learning approach that identifies pathogenic variant combinations in gene pairs (called digenic or bilocus variant combinations). We show that the results produced by this method are highly accurate and precise, an efficacy that is endorsed when validating the method on recently published independent disease-causing data. Confidence labels of 95% and 99% are identified, representing the probability of a bilocus combination being a true pathogenic result, providing geneticists with rational markers to evaluate the most relevant pathogenic combinations and limit the search space and time. Finally, the VarCoPP has been designed to act as an interpretable method that can provide explanations on why a bilocus combination is predicted as pathogenic and which biological information is important for that prediction. This work provides an important step toward the genetic understanding of rare diseases, paving the way to clinical knowledge and improved patient care.", "date": "2019-06-11T00:00:00Z", "citationCount": 48, "authors": [ { "name": "Papadimitriou S." }, { "name": "Gazzo A." }, { "name": "Versbraegen N." }, { "name": "Nachtegael C." }, { "name": "Aerts J." }, { "name": "Moreau Y." }, { "name": "Van Dooren S." }, { "name": "Nowe A." }, { "name": "Smits G." }, { "name": "Lenaerts T." } ], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } }, { "doi": "10.1186/s12859-023-05291-3", "pmid": null, "pmcid": null, "type": [], "version": "2.0", "note": null, "metadata": { "title": "Faster and more accurate pathogenic combination predictions with VarCoPP2.0", "abstract": "Background: The prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailored towards such cases can help shorten the gap of missing diagnoses and can aid researchers in dealing with the high complexity of the derived data. The predictor VarCoPP (Variant Combinations Pathogenicity Predictor) that was published in 2019 and identified potentially pathogenic variant combinations in gene pairs (bilocus variant combinations), was the first important step in this direction. Despite its usefulness and applicability, several issues still remained that hindered a better performance, such as its False Positive (FP) rate, the quality of its training set and its complex architecture. Results: We present VarCoPP2.0: the successor of VarCoPP that is a simplified, faster and more accurate predictive model identifying potentially pathogenic bilocus variant combinations. Results from cross-validation and on independent data sets reveal that VarCoPP2.0 has improved in terms of both sensitivity (95% in cross-validation and 98% during testing) and specificity (5% FP rate). At the same time, its running time shows a significant 150-fold decrease due to the selection of a simpler Balanced Random Forest model. Its positive training set now consists of variant combinations that are more confidently linked with evidence of pathogenicity, based on the confidence scores present in OLIDA, the Oligogenic Diseases Database (https://olida.ibsquare.be). The improvement of its performance is also attributed to a more careful selection of up-to-date features identified via an original wrapper method. We show that the combination of different variant and gene pair features together is important for predictions, highlighting the usefulness of integrating biological information at different levels. Conclusions: Through its improved performance and faster execution time, VarCoPP2.0 enables a more accurate analysis of larger data sets linked to oligogenic diseases. Users can access the ORVAL platform (https://orval.ibsquare.be) to apply VarCoPP2.0 on their data.", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Versbraegen N." }, { "name": "Gravel B." }, { "name": "Nachtegael C." }, { "name": "Renaux A." }, { "name": "Verkinderen E." }, { "name": "Nowe A." }, { "name": "Lenaerts T." }, { "name": "Papadimitriou S." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Tom Lenaerts", "email": "tlenaert@ulb.ac.be", "url": "http://www.ibsquare.be", "orcidid": "https://orcid.org/0000-0003-3645-1455", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sofia Papadomitriou", "email": "sofiapapad.bio@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Interuniversity Institute of Bioinformatics in Brussels", "email": null, "url": "https://ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "tlenaert@ulb.ac.be", "additionDate": "2019-07-03T15:13:23Z", "lastUpdate": "2023-07-31T11:59:09.158293Z", "editPermission": { "type": "group", "authors": [ "emmaver" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SAMtools", "description": "SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.", "homepage": "http://www.htslib.org/", "biotoolsID": "samtools", "biotoolsCURIE": "biotools:samtools", "version": [ "1.0", "1.1", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.16.1", "1.17", "1.18" ], "otherID": [], "relation": [ { "biotoolsID": "htslib", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" }, { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Suite", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Rare Disease", "Animal and Crop Genomics", "SAMtools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/samtools", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/samtools/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#howtos", "type": [ "Other" ], "note": "HowTos for samtools" }, { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null }, { "url": "http://www.htslib.org/download/", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": "19505943", "pmcid": "PMC2723002", "type": [ "Primary" ], "version": null, "note": "The Sequence Alignment/Map format and SAMtools.", "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 33651, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.", "date": "2021-02-01T00:00:00Z", "citationCount": 1611, "authors": [ { "name": "Danecek P." }, { "name": "Bonfield J.K." }, { "name": "Liddle J." }, { "name": "Marshall J." }, { "name": "Ohan V." }, { "name": "Pollard M.O." }, { "name": "Whitwham A." }, { "name": "Keane T." }, { "name": "McCarthy S.A." }, { "name": "Davies R.M." } ], "journal": "GigaScience" } }, { "doi": "10.1093/bioinformatics/btr509", "pmid": "21903627", "pmcid": "PMC3198575", "type": [], "version": null, "note": null, "metadata": { "title": "A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data", "abstract": "Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. © The Author 2011. Published by Oxford University Press. All rights reserved.", "date": "2011-11-01T00:00:00Z", "citationCount": 3386, "authors": [ { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Richard Durbin", "email": "rd@sanger.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "community": { "biolib": { "app_name": "samtools", "author_name": "SAMtools", "author_username": "samtools" } }, "owner": "awhitwham", "additionDate": "2017-01-13T13:16:12Z", "lastUpdate": "2023-07-25T13:47:20.273905Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "animalandcropgenomics", "alice", "awhitwham", "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OLIDA: OLIgogenic diseases DAtabase", "description": "OLIDA is a curated database of oligogenic diseases and the variants in genes that have been published as causing these diseases. The combinations of variants that are contained in this database have been identified by researchers as being the cause of certain genetic diseases.", "homepage": "https://olida.ibsquare.be", "biotoolsID": "olida", "biotoolsCURIE": "biotools:olida", "version": [], "otherID": [], "relation": [ { "biotoolsID": "dida", "type": "isNewVersionOf" }, { "biotoolsID": "variant_combinaton_pathogenicity_predictor", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "CC-BY-NC-4.0", "collectionID": [ "Rare Disease" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Belgium" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/DATABASE/BAAC023", "pmid": "35411390", "pmcid": "PMC9216476", "type": [], "version": null, "note": null, "metadata": { "title": "Scaling up oligogenic diseases research with OLIDA: The Oligogenic Diseases Database", "abstract": "Improving the understanding of the oligogenic nature of diseases requires access to high-quality, well-curated Findable, Accessible, Interoperable, Reusable (FAIR) data. Although first steps were taken with the development of the Digenic Diseases Database, leading to novel computational advancements to assist the field, these were also linked with a number of limitations, for instance, the ad hoc curation protocol and the inclusion of only digenic cases. The OLIgogenic diseases DAtabase (OLIDA) presents a novel, transparent and rigorous curation protocol, introducing a confidence scoring mechanism for the published oligogenic literature. The application of this protocol on the oligogenic literature generated a new repository containing 916 oligogenic variant combinations linked to 159 distinct diseases. Information extracted from the scientific literature is supplemented with current knowledge support obtained from public databases. Each entry is an oligogenic combination linked to a disease, labelled with a confidence score based on the level of genetic and functional evidence that supports its involvement in this disease. These scores allow users to assess the relevance and proof of pathogenicity of each oligogenic combination in the database, constituting markers for reporting improvements on disease-causing oligogenic variant combinations. OLIDA follows the FAIR principles, providing detailed documentation, easy data access through its application programming interface and website, use of unique identifiers and links to existing ontologies. Database URL: https://olida.ibsquare.be", "date": "2022-01-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Nachtegael C." }, { "name": "Gravel B." }, { "name": "Dillen A." }, { "name": "Smits G." }, { "name": "Nowe A." }, { "name": "Papadimitriou S." }, { "name": "Lenaerts T." } ], "journal": "Database" } } ], "credit": [ { "name": "Sofia Papadimitriou", "email": "sofia.papadimitriou@ulb.be", "url": null, "orcidid": "https://orcid.org/0000-0002-5057-4331", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Tom Lenaerts", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3645-1455", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Ann Nowé", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-6346-4564", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Guillaume Smits", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2845-6758", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "Jennifer", "additionDate": "2022-07-26T11:01:58.486446Z", "lastUpdate": "2023-07-18T09:08:53.869191Z", "editPermission": { "type": "group", "authors": [ "emmaver" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "WS-SNPs-and-GO", "description": "A web server for predicting disease associated variations from protein sequence and structure.", "homepage": "http://snps.biofold.org/snps-and-go", "biotoolsID": "ws_snps_and_go", "biotoolsCURIE": "biotools:ws_snps_and_go", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1467", "term": "Protein chain" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1176", "term": "GO concept ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2209", "term": "Mutation ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "SNPs&GO 3D", "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://hub.docker.com/r/biofold/snps-and-go", "type": "Container file", "note": null, "version": "2.0" } ], "documentation": [ { "url": "http://snps.biofold.org/snps-and-go/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-12-S4-S3", "pmid": "21992054", "pmcid": "PMC3194195", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "Improving the prediction of disease-related variants using protein three-dimensional structure", "abstract": "Background: Single Nucleotide Polymorphisms (SNPs) are an important source of human genome variability. Non-synonymous SNPs occurring in coding regions result in single amino acid polymorphisms (SAPs) that may affect protein function and lead to pathology. Several methods attempt to estimate the impact of SAPs using different sources of information. Although sequence-based predictors have shown good performance, the quality of these predictions can be further improved by introducing new features derived from three-dimensional protein structures.Results: In this paper, we present a structure-based machine learning approach for predicting disease-related SAPs. We have trained a Support Vector Machine (SVM) on a set of 3,342 disease-related mutations and 1,644 neutral polymorphisms from 784 protein chains. We use SVM input features derived from the protein's sequence, structure, and function. After dataset balancing, the structure-based method (SVM-3D) reaches an overall accuracy of 85%, a correlation coefficient of 0.70, and an area under the receiving operating characteristic curve (AUC) of 0.92. When compared with a similar sequence-based predictor, SVM-3D results in an increase of the overall accuracy and AUC by 3%, and correlation coefficient by 0.06. The robustness of this improvement has been tested on different datasets and in all the cases SVM-3D performs better than previously developed methods even when compared with PolyPhen2, which explicitly considers in input protein structure information.Conclusion: This work demonstrates that structural information can increase the accuracy of disease-related SAPs identification. Our results also quantify the magnitude of improvement on a large dataset. This improvement is in agreement with previously observed results, where structure information enhanced the prediction of protein stability changes upon mutation. Although the structural information contained in the Protein Data Bank is limiting the application and the performance of our structure-based method, we expect that SVM-3D will result in higher accuracy when more structural date become available. © 2011 Capriotti; licensee BioMed Central Ltd.", "date": "2011-07-05T00:00:00Z", "citationCount": 90, "authors": [ { "name": "Capriotti E." }, { "name": "Altman R.B." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1002/humu.21047", "pmid": "19514061", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Functional annotations improve the predictive score of human disease-related mutations in proteins", "abstract": "Single nucleotide polymorphisms (SNPs) are the simplest and most frequent form of human DNA variation, also valuable as genetic markers of disease susceptibility. The most investigated SNPs are missense mutations resulting in residue substitutions in the protein. Here we propose SNPs&GO, an accurate method that, starting from a protein sequence, can predict whether a mutation is disease related or not by exploiting the protein functional annotation. The scoring efficiency of SNPs&GO is as high as 82%, with a Matthews correlation coefficient equal to 0.63 over a wide set of annotated nonsynonymous mutations in proteins, including 16,330 disease-related and 17,432 neutral polymorphisms. SNPs&GO collects in unique framework information derived from protein sequence, evolutionary information, and function as encoded in the Gene Ontology terms, and outperforms other available predictive methods. © 2009 Wiley-Liss, Inc.", "date": "2009-08-01T00:00:00Z", "citationCount": 453, "authors": [ { "name": "Calabrese R." }, { "name": "Capriotti E." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Human Mutation" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://www.biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Developer" ], "note": null }, { "name": "Emidio Capriotti", "email": "emidio.capriotti@gmail.com", "url": null, "orcidid": "http://orcid.org/0000-0002-2323-0963", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Rita Casadio", "email": "casadio@biocomp.unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2017-03-01T16:16:45Z", "lastUpdate": "2023-04-21T12:34:15.309346Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "ELIXIR-ITA-BOLOGNA", "emidio" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BridgeDb", "description": "BridgeDb is a framework to map identifiers between various databases. It includes a Java library that provides an API to work with identifier-identifier mapping databases and resources.", "homepage": "http://bridgedb.github.io/", "biotoolsID": "bridgedb", "biotoolsCURIE": "biotools:bridgedb", "version": [ "3.0.18" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "note": "API for converting gene identifiers (Ensembl, Entrez) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1086", "term": "Compound identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1086", "term": "Compound identifier" }, "format": [] } ], "note": "API for converting compound identifiers (HMDB, ChEBI, ChemSpider, PubChem, etc) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.", "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_2840", "term": "Toxicology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "Apache-2.0", "collectionID": [ "Proteomics", "BIGCAT-UM", "Rare Disease", "BridgeDb", "ELIXIR-NL" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Interoperability" ], "elixirNode": [ "Netherlands" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://bridgedb.github.io/pages/docs.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-319-11964-9_7", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": null, "pmid": "20047655", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The BridgeDb framework: Standardized access to gene, protein and metabolite identifier mapping services", "abstract": "Background: Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services.Results: Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications.Conclusion: By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org. © 2010 van Iersel et al; licensee BioMed Central Ltd.", "date": "2010-01-04T00:00:00Z", "citationCount": 115, "authors": [ { "name": "van Iersel M.P." }, { "name": "Pico A.R." }, { "name": "Kelder T." }, { "name": "Gao J." }, { "name": "Ho I." }, { "name": "Hanspers K." }, { "name": "Conklin B.R." }, { "name": "Evelo C.T." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.3897/rio.8.e83031", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Gladstone Institutes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Maastricht University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Manchester University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Heroit Watt University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "maastrichtuniversity.nl", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "https://groups.google.com/forum/#!forum/bridgedb-discuss", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "egonw", "additionDate": "2015-12-01T16:27:10Z", "lastUpdate": "2023-04-06T11:32:52.646035Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "ChrisEvelo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RVS", "description": "Detection of rare disease variants in extended pedigrees using RVS.\n\nComputes estimates of the probability of related individuals sharing a rare variant.\n\nRare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).\n\nExomeSeq, Genetics, GenomeWideAssociation, ImmunoOncology, Software, VariantDetection, WholeGenome.", "homepage": "https://bioconductor.org/packages/release/bioc/html/RVS.html", "biotoolsID": "rvs_software", "biotoolsCURIE": "biotools:rvs_software", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_3791", "term": "Collapsing methods" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "Rare Disease" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTY976", "pmid": "30500888", "pmcid": "PMC6612888", "type": [], "version": null, "note": null, "metadata": { "title": "Detection of rare disease variants in extended pedigrees using RVS", "abstract": "© 2018 The Author(s) 2018. Published by Oxford University Press.Summary: Family-based sequencing studies enable researchers to identify highly penetrant genetic variants too rare to be tested in conventional case-control studies, by studying co-segregation of variant and disease phenotypes. When multiple affected subjects in a family are sequenced, the probability that a variant or a set of variants is shared identical-by-descent by some or all affected relatives provides evidence against the null hypothesis of complete absence of linkage and association. The Rare Variant Sharing software package RVS implements a suite of tools to assess association and linkage between rare genetic variants and a dichotomous disease indicator in family pedigrees. Availability and Implementation: RVS is available as open source software from the Bioconductor webpage at https://bioconductor.org/packages/release/bioc/html/RVS.html. Supplementary information: Supplementary data are available at Bioinformatics online.", "date": "2019-07-15T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Sherman T." }, { "name": "Fu J." }, { "name": "Scharpf R.B." }, { "name": "Bureau A." }, { "name": "Ruczinski I." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Ingo Ruczinski", "email": "ingo@jhu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Jennifer", "additionDate": "2023-02-13T20:20:42.025598Z", "lastUpdate": "2023-02-13T20:20:42.028161Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "RD-Connect Genome-Phenome Analysis Platform (GPAP)", "description": "An online tool for diagnosis and gene discovery in rare disease research. The platform features allow identifying disease-causing mutations in rare disease patients and linking them with detailed clinical information.", "homepage": "https://platform.rd-connect.eu/", "biotoolsID": "rd-connect_platform", "biotoolsCURIE": "biotools:rd-connect_platform", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" }, { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease", "ELIXIR-ES", "INB", "RIS3CAT VEIS" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1002/humu.24353", "pmid": "35178824", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases", "abstract": "© 2022 The Authors. Human Mutation published by Wiley Periodicals LLC.Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.", "date": "2022-06-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Laurie S." }, { "name": "Piscia D." }, { "name": "Matalonga L." }, { "name": "Corvo A." }, { "name": "Fernandez-Callejo M." }, { "name": "Garcia-Linares C." }, { "name": "Hernandez-Ferrer C." }, { "name": "Luengo C." }, { "name": "Martinez I." }, { "name": "Papakonstantinou A." }, { "name": "Pico-Amador D." }, { "name": "Protasio J." }, { "name": "Thompson R." }, { "name": "Tonda R." }, { "name": "Bayes M." }, { "name": "Bullich G." }, { "name": "Camps-Puchadas J." }, { "name": "Paramonov I." }, { "name": "Trotta J.-R." }, { "name": "Alonso A." }, { "name": "Attimonelli M." }, { "name": "Beroud C." }, { "name": "Bros-Facer V." }, { "name": "Buske O.J." }, { "name": "Canada-Pallares A." }, { "name": "Fernandez J.M." }, { "name": "Hansson M.G." }, { "name": "Horvath R." }, { "name": "Jacobsen J.O.B." }, { "name": "Kaliyaperumal R." }, { "name": "Lair-Preterre S." }, { "name": "Licata L." }, { "name": "Lopes P." }, { "name": "Lopez-Martin E." }, { "name": "Mascalzoni D." }, { "name": "Monaco L." }, { "name": "Perez-Jurado L.A." }, { "name": "Posada de la Paz M." }, { "name": "Rambla J." }, { "name": "Rath A." }, { "name": "Riess O." }, { "name": "Robinson P.N." }, { "name": "Salgado D." }, { "name": "Smedley D." }, { "name": "Spalding D." }, { "name": "'t Hoen P.A.C." }, { "name": "Topf A." }, { "name": "Zaharieva I." }, { "name": "Graessner H." }, { "name": "Gut I.G." }, { "name": "Lochmuller H." }, { "name": "Beltran S." } ], "journal": "Human Mutation" } }, { "doi": "10.1007/s11606-014-2908-8", "pmid": "25029978", "pmcid": "PMC4124112", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "RD-connect: An integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research", "abstract": "Research into rare diseases is typically fragmented by data type and disease. Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype, genomic data, biomaterial availability, and research/trial data sets. Such data must be linked at both an individual-patient and whole-cohort level to enable researchers to gain a complete view of their disease and patient population of interest. Data access and authorization procedures are required to allow researchers in multiple institutions to securely compare results and gain new insights. Funded by the European Union's Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseases. © 2014 Society of General Internal Medicine.", "date": "2014-01-01T00:00:00Z", "citationCount": 133, "authors": [ { "name": "Thompson R." }, { "name": "Johnston L." }, { "name": "Taruscio D." }, { "name": "Monaco L." }, { "name": "Beroud C." }, { "name": "Gut I.G." }, { "name": "Hansson M.G." }, { "name": "T Hoen P.-B.A." }, { "name": "Patrinos G.P." }, { "name": "Dawkins H." }, { "name": "Ensini M." }, { "name": "Zatloukal K." }, { "name": "Koubi D." }, { "name": "Heslop E." }, { "name": "Paschall J.E." }, { "name": "Posada M." }, { "name": "Robinson P.N." }, { "name": "Bushby K." }, { "name": "Lochmuller H." } ], "journal": "Journal of General Internal Medicine" } } ], "credit": [ { "name": "Steven Laurie", "email": "steven.laurie@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Davide Piscia", "email": "davide.piscia@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Leslie Matalonga", "email": "leslie.matalonga@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Alberto Corvó", "email": "alberto.corvo@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Marcos Fernández-Callejo", "email": "marcos.fernandez@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Carles Garcia-Linares", "email": "carles.garcia@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez@cnag.crg.eu", "url": "http://www.carleshf.com", "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Cristina Luengo", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Inés Martínez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Anastasios Papakonstantinou", "email": "anastasios.papakonstantinou@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Daniel Picó-Amador", "email": "daniel.pico@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Joan Protasio", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Rachel Thompson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Raul Tonda", "email": "raul.tonda@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Mònica Bayés", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Gemma Bullich", "email": "gemma.bullich@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jordi Camps-Puchadas", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ida Paramonov", "email": "ida.paramonov@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jean-Rémi Trotta", "email": "jeanremi.trotta@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Angel Alonso", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Marcella Attimonelli", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Christophe Béroud", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Virginie Bros-Facer", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Orion J. Buske", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Andrés Cañada-Pallarés", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "José M. Fernández", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Mats G. Hansson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Rita Horvath", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Julius O.B. 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