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Data can be uploaded as a file or by copy-pasteing it to the text box.", "homepage": "http://biit.cs.ut.ee/clustvis", "biotoolsID": "clustvis", "biotoolsCURIE": "biotools:clustvis", "version": [ "1" ], "otherID": [ { "value": "RRID:SCR_017133", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0313", "term": "Gene expression clustering" }, { "uri": "http://edamontology.org/operation_2942", "term": "Treemap visualisation" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" }, { "uri": "http://edamontology.org/operation_2939", "term": "Principal component plotting" }, { "uri": "http://edamontology.org/operation_0531", "term": "Heat map generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3111", "term": "Processed microarray data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] }, { "data": { "uri": "http://edamontology.org/data_3113", "term": "Sample annotation" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Elixir-EE" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Estonia" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/taunometsalu/ClustVis", "type": [ "Repository" ], "note": "A code repository in github." } ], "download": [ { "url": "https://hub.docker.com/r/taunometsalu/clustvis/", "type": "Container file", "note": "Docker image", "version": null } ], "documentation": [ { "url": "https://biit.cs.ut.ee/clustvis/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv468", "pmid": "25969447", "pmcid": "PMC4489295", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ClustVis: A web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap", "abstract": "The Principal Component Analysis (PCA) is a widely used method of reducing the dimensionality of highdimensional data, often followed by visualizing two of the components on the scatterplot. Although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. The same applies to creating heatmaps: it is possible to add conditional formatting for Excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. We present a web tool called ClustVis that aims to have an intuitive user interface. Users can upload data from a simple delimited text file that can be created in a spreadsheet program. It is possible to modify data processing methods and the final appearance of the PCA and heatmap plots by using drop-down menus, text boxes, sliders etc. Appropriate defaults are given to reduce the time needed by the user to specify input parameters. As an output, users can download PCA plot and heatmap in one of the preferred file formats. This web server is freely available at http://biit.cs.ut.ee/clustvis/.", "date": "2015-01-01T00:00:00Z", "citationCount": 2504, "authors": [ { "name": "Metsalu T." }, { "name": "Vilo J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "ELIXIR-EE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Tauno Metsalu", "email": "tauno.metsalu@ut.ee", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "biit.support@ut.ee", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "user.1781877465", "additionDate": "2015-01-22T11:13:24Z", "lastUpdate": "2026-07-02T09:12:33.297394Z", "editPermission": { "type": "group", "authors": [ "may.kay" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SequenceMatrix", "description": "Concatenation software for the fast assembly of multi-gene datasets with character set and codon information.", "homepage": "http://www.ggvaidya.com/taxondna/", "biotoolsID": "sequencematrix", "biotoolsCURIE": "biotools:sequencematrix", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "GPL-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/gaurav/taxondna", "type": [ "Repository" ], "note": null }, { "url": "http://taxondna.sourceforge.net", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1111/J.1096-0031.2010.00329.X", "pmid": "34875773", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "SequenceMatrix: Concatenation software for the fast assembly of multi-gene datasets with character set and codon information", "abstract": "We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases (\"Ns\"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from © The Willi Hennig Society 2010. © The Willi Hennig Society 2010.", "date": "2011-04-01T00:00:00Z", "citationCount": 1348, "authors": [ { "name": "Vaidya G." }, { "name": "Lohman D.J." }, { "name": "Meier R." } ], "journal": "Cladistics" } } ], "credit": [ { "name": "Rudolf Meier", "email": "meier@nus.edu.sg", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "David J. 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The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories are also incorporated.", "homepage": "http://mmb.irbbarcelona.org/MDWeb2", "biotoolsID": "mdweb", "biotoolsCURIE": "biotools:mdweb", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": "Platform for setup and analysis of molecular dynamics simulations", "cmd": null } ], "toolType": [ "Web application", "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_3306", "term": "Biophysics" }, { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Linux" ], "language": [ "PHP" ], "license": null, "collectionID": [ "BioExcel", "IRB-BSC", "ELIXIR-ES" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://mmb.irbbarcelona.org/MDWeb2/help.php?id=base", "type": [ "User manual", "Training material" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts139", "pmid": "22437851", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MDWeb and MDMoby: An integrated web-based platform for molecular dynamics simulations", "abstract": "MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-05-01T00:00:00Z", "citationCount": 147, "authors": [ { "name": "Hospital A." }, { "name": "Andrio P." }, { "name": "Fenollosa C." }, { "name": "Cicin-Sain D." }, { "name": "Orozco M." }, { "name": "Gelpi J.L." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Institute of Research in Biomedicine - Barcelona", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Institute for Research in Biomedicine Barcelona", "email": "mdweb@mmb.irbbarcelona.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jdianes", "additionDate": "2016-10-03T14:08:36Z", "lastUpdate": "2026-07-02T09:12:20.161140Z", "editPermission": { "type": "group", "authors": [ "adam.hospital@irbbarcelona.org", "gelpi@ub.edu", "rutupatel" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BIGR xnattools", "description": "xnattools is a python package with a set of modules for performing various operations on data stored in XNAT servers. The main purpose is to provide one standardized platform for running operations on XNAT servers. 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