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{ "count": 30608, "next": "?page=2", "previous": null, "list": [ { "name": "bmtagger", "description": "Best Match Tagger for removing contaminant reads from metagenomics datasets", "homepage": "https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/", "biotoolsID": "bmtagger", "biotoolsCURIE": "biotools:bmtagger", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3219", "term": "Read pre-processing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [], "owner": "m.bernt", "additionDate": "2025-11-06T15:12:25.197235Z", "lastUpdate": "2025-11-06T15:12:25.199795Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "prolfquapp", "description": "A command-line tool for differential expression analysis in quantitative proteomics", "homepage": "https://github.com/prolfqua/prolfquapp", "biotoolsID": "prolfquapp", "biotoolsCURIE": "biotools:prolfquapp", "version": [ "0.1.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": "./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN\n# and again you run the version within the docker container with\n# ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN" }, { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": 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[ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/prolfqua/prolfquapp", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/prolfqua/prolfquapp/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6", "type": "Downloads page", "note": null, "version": "0.1.6" } ], "documentation": [ { "url": "https://github.com/prolfqua/prolfquapp/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.4c00911", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "0.0.6", "note": null, "metadata": { "title": "prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics", "abstract": "", "date": "2025-02-07T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Journal of Proteome Research" } } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2025-02-28T15:04:33.594183Z", "lastUpdate": "2025-11-06T14:37:12.116175Z", "editPermission": { "type": "group", "authors": [ "thatmariia" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Feature-based harmonization", "description": "The tool is designed to perform harmonization at the feature-level. Feature-based harmonization method aims to reduce the variability in the radiomics features due to different scanners, acquisition protocols and conditions by using empirical Bayesian methods to estimate differences in radiomics values and then expressing them in a common space (location/scale adjustment). The tool offers two methods: (1) ComBat method, which shifts the radiomics features to the overall mean and pooled variance of all centers, and (2) M-ComBat method, which shifts the radiomics features to the mean and variance of the chosen reference center with the most samples.", "homepage": "https://cbml-gitlab.ics.forth.gr/adovrou/featuresharmonization/-/tree/eucaim?ref_type=heads", "biotoolsID": "feature-based_harmonization", "biotoolsCURIE": "biotools:feature-based_harmonization", "version": [ "1.4" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "eucaim" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://cbml-gitlab.ics.forth.gr/adovrou/featuresharmonization/-/tree/eucaim?ref_type=heads", "type": [ "Repository" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/feat_harmonization/artifacts-tab", "type": [ "Other" ], "note": "Link to EUCAIM's harbor" } ], "download": [], "documentation": [ { "url": "https://cbml-gitlab.ics.forth.gr/adovrou/featuresharmonization/-/tree/eucaim?ref_type=heads", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [ { "name": "Aikaterini Dovrou", "email": "dovrou@ics.forth.gr", "url": null, "orcidid": "https://orcid.org/0000-0001-5242-6060", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "adovrou", "additionDate": "2025-10-30T12:18:23.489392Z", "lastUpdate": "2025-11-06T10:01:42.643613Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Biologically motivated normalization techniques", "description": "The tool is designed to perform normalization at the image-level. This normalization method aims to reduce the variability in the intensity values of the Magnetic Resonance (MR) prostate images due to different scanners, acquisition protocols and conditions, based on the intensity values of specific tissues. This tool implements three biologically-motivated intensity normalization techniques: (1) The fat-based normalization method, (2) The muscle-based normalization method, and (3) The single tissue (fat or muscle) piece-wise normalization method.", "homepage": "https://cbml-gitlab.ics.forth.gr/adovrou/biointensitynorm/-/tree/eucaim?ref_type=heads", "biotoolsID": "biologically_motivated_normalization_techniques", "biotoolsCURIE": "biotools:biologically_motivated_normalization_techniques", "version": [ "1.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "eucaim" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://cbml-gitlab.ics.forth.gr/adovrou/biointensitynorm/-/tree/eucaim?ref_type=heads", "type": [ "Repository" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/bio_intensity_norm/artifacts-tab", "type": [ "Other" ], "note": "Link to EUCAIM's Harbor" } ], "download": [], "documentation": [ { "url": "https://cbml-gitlab.ics.forth.gr/adovrou/biointensitynorm/-/tree/eucaim?ref_type=heads", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [ { "name": "Aikaterini Dovrou", "email": "dovrou@ics.forth.gr", "url": null, "orcidid": "https://orcid.org/0000-0001-5242-6060", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "adovrou", "additionDate": "2025-10-30T11:34:24.728018Z", "lastUpdate": "2025-11-06T09:42:46.820448Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "N4 Bias Filter", "description": "The tool is designed to perform image pre-processing to reduce the bias field effect, improving the quality of the image. Two main functionalities are offered: (1) Apply N4 filter to image/images (either with the default parameters values or with parameters values defined by the user) (2) Find the optimal configuration of the N4 filter for specific image/images by measuring the Full Width at Half Maximum (FWHM) of the periprostatic fat distribution.", "homepage": "https://cbml-gitlab.ics.forth.gr/adovrou/n4biasfilter/-/tree/eucaim?ref_type=heads", "biotoolsID": "n4_bias_filter", "biotoolsCURIE": "biotools:n4_bias_filter", "version": [ "1.7" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3671", "term": "Text" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "eucaim" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://cbml-gitlab.ics.forth.gr/adovrou/n4biasfilter/-/tree/eucaim?ref_type=heads", "type": [ "Repository" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/n4filter/artifacts-tab", "type": [ "Other" ], "note": "Link to EUCAIM's harbor" } ], "download": [], "documentation": [ { "url": "https://cbml-gitlab.ics.forth.gr/adovrou/n4biasfilter/-/tree/eucaim?ref_type=heads", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1016/j.mri.2023.03.012", "pmid": "37004467", "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "A segmentation-based method improving the performance of N4 bias field correction on T2weighted MR imaging data of the prostate", "abstract": "", "date": "2023-09-01T00:00:00Z", "citationCount": 23, "authors": [], "journal": "Magnetic Resonance Imaging" } } ], "credit": [ { 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], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Metabolic network modelling" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://waschina.github.io/cobrar/", "type": [ "Other" ], "note": "Link to the GitHub repo added" } ], "download": [ { "url": "https://waschina.github.io/cobrar/", "type": "Source code", "note": null, "version": "0.2.2" } ], "documentation": [], "publication": [], "credit": [ { "name": "Silvio Waschina", "email": "s.waschina@nutrinf.uni-kiel.de", "url": "https://www.uni-kiel.de/en/person/waschina-silvio-44493", "orcidid": "https://orcid.org/0000-0002-6290-3593", 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