Resource List
List all resources, or create a new resource.
GET /api/t/?format=api
{ "count": 30585, "next": "?page=2", "previous": null, "list": [ { "name": "Pediatric Brain Tumor Segmenter", "description": "The Pediatric Brain Tumor Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of pediatric brain tumors in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric brain MRIs to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://segmenter.hope4kids.io/", "biotoolsID": "pediatric_brain_tumor_segmenter", "biotoolsCURIE": "biotools:pediatric_brain_tumor_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-SA-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-10-28T18:31:05.926498Z", "lastUpdate": "2025-10-28T18:39:57.123169Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NetStart", "description": "Prediction of eukaryotic translation initiation sites using a protein language model.\n\nNetStart 2.0 is a deep learning-based model that predicts canonical translation initiation sites in mRNA transcripts in species across the eukaryotic domain, including vertebrates, invertebrates, plants, fungi, and protists. \n\nThe model integrates the ESM-2 protein language model for assessing transitions from non-coding to coding regions with local start codon sequence context and taxonomical information. It has been trained on sequences from 60 phylogenetically diverse eukaryotic species.\n\nIf you need help with the bioinformatics programs, see the \"Getting Help\" section at the server site at the link.", "homepage": "https://services.healthtech.dtu.dk/services/NetStart-2.0/", "biotoolsID": "netstart_2.0", "biotoolsCURIE": "biotools:netstart_2.0", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_0439", "term": "Translation initiation site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/lsandvad/netstart2", "type": [ "Repository" ], "note": "GitHub with code and instructions and to download and run the program locally" }, { "url": "https://services.healthtech.dtu.dk/services/NetStart-2.0/", "type": [ "Service" ], "note": "NetStart 2.0 server where sequences can be uploaded directly without having to download the program (hosted by DTU Health Tech)." } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/S12859-025-06220-2", "pmid": "40830753", "pmcid": "PMC12366053", "type": [ "Method" ], "version": "2.0", "note": null, "metadata": { "title": "NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Line Sandvad Nielsen", "email": "line.s.nielsen@bio.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Henrik Nielsen", "email": "henni@dtu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "linesandvad", "additionDate": "2025-10-27T16:27:24.014603Z", "lastUpdate": "2025-10-28T17:34:39.042070Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "StripePy", "description": "StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning", "homepage": "https://github.com/paulsengroup/StripePy", "biotoolsID": "stripepy", "biotoolsCURIE": "biotools:stripepy", "version": [ "0.0.1", "0.0.2", "1.0.0", "1.1.0", "1.1.1", "1.2.0", "1.2.1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/paulsengroup/StripePy/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/paulsengroup/StripePy/discussions", "type": [ "Discussion forum" ], "note": null }, { "url": "https://github.com/paulsengroup/StripePy.git", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/paulsengroup/StripePy/releases", "type": "Source code", "note": null, "version": null }, { "url": "https://hub.docker.com/r/paulsengroup/stripepy", "type": "Container file", "note": null, "version": null }, { "url": "https://doi.org/10.5281/zenodo.14283921", "type": "Test data", "note": null, "version": null }, { "url": "https://pypi.org/project/stripepy-hic/", "type": "Binaries", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/stripepy-hic", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://stripepy.readthedocs.io/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2024.12.20.629789", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btaf351", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "StripePy: fast and robust characterization of architectural stripes", "abstract": "", "date": "2025-06-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Bioinformatics" } } ], "credit": [], "owner": "robomics", "additionDate": "2024-12-21T15:24:55.662209Z", "lastUpdate": "2025-10-28T12:14:50.951141Z", "editPermission": { "type": "group", "authors": [ "rea1991" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PTM-CrossTalkMapper", "description": "Visualization of the Dynamics of Histone Modifications and Their Crosstalk Using PTM-CrossTalkMapper.\n\nR scripts to create crosstalk maps that visualize multi-layered proteoform data.\n\nPTM-CrossTalkMapper is a flexible toolkit to visualize multi-layered quantitative post-transcriptional modification (PTM) data. The preprint manuscript can be found on bioRxiv", "homepage": "https://github.com/veitveit/CrossTalkMapper", "biotoolsID": "PTM-CrossTalkMapper", "biotoolsCURIE": "biotools:PTM-CrossTalkMapper", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_0417", "term": "Post-translation modification site prediction" }, { "uri": "http://edamontology.org/operation_3755", "term": "PTM localisation" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/veitveit/CrossTalkMapper?tab=readme-ov-file#documentation", "type": [ "General" ], "note": null }, { "url": "https://link.springer.com/protocol/10.1007/978-1-0716-2317-6_13", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.ymeth.2020.01.012", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Visualization of the dynamics of histone modifications and their crosstalk using PTM-CrossTalkMapper", "abstract": "", "date": "2020-12-01T00:00:00Z", "citationCount": 17, "authors": [], "journal": "Methods" } } ], "credit": [], "owner": "Pub2Tools", "additionDate": "2020-01-09T17:51:22Z", "lastUpdate": "2025-10-27T17:06:26.845284Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Thor", "description": "Spatial transcriptomics integrates transcriptomics data with histological tissue images, offering deeper insights into cellular organization and molecular functions. However, existing computational platforms mainly focus on genomic analysis, leaving a gap in the seamless integration of genomic and imaging modalities. Thor is a comprehensive spatial transcriptomics analysis tool designed to bridge this gap by enabling efficient co-analysis of gene expression profiles and high-resolution tissue images. It provides scalable workflows for spatial feature extraction, cell segmentation, gene–spatial correlation, and visualization, facilitating multi-omic insights into tissue architecture and cellular heterogeneity.", "homepage": "https://github.com/GuangyuWangLab2021/Thor", "biotoolsID": "Thor", "biotoolsCURIE": "biotools:Thor", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" }, { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://wanglab.tech/thor", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://wanglab.tech/thor/", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.21203/RS.3.RS-4909620/V1", "pmid": "40162205", "pmcid": "PMC11952649", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Pengzhi Zhang", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-6920-1490", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Weiqing Chen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3539-9210", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "udayaraja", "additionDate": "2025-10-27T16:15:48.531662Z", "lastUpdate": "2025-10-27T16:59:57.862356Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TEtranscripts", "description": "TEtranscripts is a software package for including transposable elements in differential expression analysis of RNA-seq datasets. It assigns reads to genes and transposable elements, performs differential expression testing, and provides statistical analysis for transposable element expression.", "homepage": "https://hammelllab.labsites.cshl.edu/software/#TEtranscripts", "biotoolsID": "tetranscripts", "biotoolsCURIE": "biotools:tetranscripts", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Gene expression data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "TEtranscripts --mode TE --input <input_file> --output <output_file>" } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/mhammell-laboratory/TEtranscripts", "type": [ "Repository" ], "note": null }, { "url": "https://www.mghlab.org/software/tetranscripts", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/mhammell-laboratory/TEtranscripts", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/mhammell-laboratory/TEtranscripts", "type": [ "Installation instructions", "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv422", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets", "abstract": "", "date": "2015-05-25T00:00:00Z", "citationCount": 419, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Molly Gale Hammell", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0405-8392", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "samuelruizperez", "additionDate": "2025-10-27T16:45:48.395441Z", "lastUpdate": "2025-10-27T16:50:09.756484Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NetworkX", "description": "Exploring Network Structure, Dynamics, and Function using NetworkX.\n\nSoftware for Complex Networks — NetworkX 3.5.1rc0.dev0 documentation.\n\nNetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. It provides:.\n\nWith NetworkX you can load and store networks in standard and nonstandard data formats, generate many types of random and classic networks, analyze network structure, build network models, design new network algorithms, draw networks, and much more.", "homepage": "https://networkx.org/documentation/latest/", "biotoolsID": "NetworkX", "biotoolsCURIE": "biotools:NetworkX", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0605", "term": "Informatics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.25080/TCWV9851", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "Julia.Villarroel", "additionDate": "2025-10-27T16:45:07.895751Z", "lastUpdate": "2025-10-27T16:45:07.898233Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SPACE", "description": "STRING proteins as complementary embeddings.\n\nMotivation Representation learning has revolutionized sequence-based prediction of protein function and subcellular localization. Protein networks are an important source of information complementary to sequences, but the use of protein networks has proven to be challenging in the context of machine learning, especially in a cross-species setting. Results. We leveraged the STRING database of protein networks and orthology relations for 1322 eukaryotes to generate network-based cross-species protein embeddings. We did this by first creating species-specific network embeddings and subsequently aligning them based on orthology relations to facilitate direct cross-species comparisons", "homepage": "https://github.com/deweihu96/SPACE", "biotoolsID": "string-space", "biotoolsCURIE": "biotools:string-space", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" }, { "uri": "http://edamontology.org/operation_3094", "term": "Protein interaction network prediction" }, { "uri": "http://edamontology.org/operation_2489", "term": "Subcellular localisation prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAF496", "pmid": "40924541", "pmcid": "PMC12453690", "type": [], "version": null, "note": null, "metadata": { "title": "SPACE: STRING proteins as complementary embeddings", "abstract": "", "date": "2025-09-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Dewei Hu", "email": "larsjuhl.jensen@zs.com", "url": null, "orcidid": "https://orcid.org/0009-0005-5823-1498", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "deweihu", "additionDate": "2025-10-27T16:11:34.389774Z", "lastUpdate": "2025-10-27T16:11:34.392675Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NucleoATAC", "description": "Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.\n\nThis package is no longer being actively maintained; feel free to post issues that others in the community may respond to, but this package will likely not be updated further. Additionally, if anyone wants to maintain a fork of the package or has developed an alternative package for similar purposes, would be happy to link to that repo here.\n\n2025 Python Packaging Survey is now live!.\n\nPlease cite our paper at Genome Research if you use this tool in your research.\n\nNew Authentication Rolling Out - We're upgrading our sign-in process to give you one account across all Anaconda products! Browser users will see a refreshed sign-in flow, while CLI users will experience no changes.\n\nHome: http://nucleoatac.readthedocs.io/en/latest/.\n\nDocumentation can be found at http://nucleoatac.readthedocs.org/en/latest/.\n\nPython package for calling nucleosomes using ATAC-Seq data.", "homepage": "https://anaconda.org/bioconda/nucleoatac", "biotoolsID": "nucleoatac", "biotoolsCURIE": "biotools:nucleoatac", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3222", "term": "Peak calling" }, { "uri": "http://edamontology.org/operation_0438", "term": "Transcriptional regulatory element prediction" }, { "uri": "http://edamontology.org/operation_0432", "term": "Nucleosome position prediction" }, { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3176", "term": "DNA packaging" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" }, { "uri": "http://edamontology.org/topic_3940", "term": "Chromosome conformation capture" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/GreenleafLab/NucleoATAC", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://nucleoatac.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/GR.192294.115", "pmid": "26314830", "pmcid": "PMC4617971", "type": [], "version": null, "note": null, "metadata": { "title": "Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions", "abstract": "", "date": "2015-11-01T00:00:00Z", "citationCount": 246, "authors": [], "journal": "Genome Research" } } ], "credit": [], "owner": "satroz", "additionDate": "2025-10-27T16:07:12.131271Z", "lastUpdate": "2025-10-27T16:07:12.133668Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MS Annika", "description": "MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer.", "homepage": "https://github.com/hgb-bin-proteomics/MSAnnika", "biotoolsID": "ms_annika", "biotoolsCURIE": "biotools:ms_annika", "version": [ "Proteome Discoverer 3.2: MS Annika 3.0 v3.0.7", "Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7", "Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fix", "Proteome Discoverer 2.5: MS Annika 2.0 v1.1.3", "Proteome Discoverer 2.4: MS Annika v1.0.0", "Proteome Discoverer 2.3: MS Annika v1.0.0" ], "otherID": [], "relation": [ { "biotoolsID": "ms_amanda", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3755", "term": "PTM localisation" }, { "uri": "http://edamontology.org/operation_3645", "term": "PTM identification" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3712", "term": "Thermo RAW" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Windows" ], "language": [ "C#" ], "license": "Freeware", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/hgb-bin-proteomics/MSAnnika", "type": [ "Repository" ], "note": "MS Annika version archive" } ], "download": [ { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.2/latest.zip", "type": "Software package", "note": "Latest MS Annika version for Proteome Disoverer 3.2", "version": "PD3.2:latest" }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip", "type": "Software package", "note": "Latest MS Annika version for Proteome Disoverer 3.1", "version": "PD3.1:latest" }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zip", "type": "Software package", "note": "Latest MS Annika version for Proteome Disoverer 3.0", "version": "PD3.0:latest" }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zip", "type": "Software package", "note": "Latest MS Annika version for Proteome Disoverer 2.5", "version": "PD2.5:latest" } ], "documentation": [ { "url": "https://hgb-bin-proteomics.github.io/MSAnnika/", "type": [ "General" ], "note": null }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/MS_Annika_3.0_UserManual.pdf", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/tutorial/MS_Annika_3.0_Tutorial.pdf", "type": [ "Training material" ], "note": "Detailed tutorial how to use MS Annika" }, { "url": "https://www.youtube.com/watch?v=L1lVt35PYv4", "type": [ "Training material" ], "note": "Detailed tutorial how to use MS Annika" } ], "publication": [ { "doi": "10.1021/acs.jproteome.0c01000", "pmid": "33852321", "pmcid": "PMC8155564", "type": [ "Primary" ], "version": "1.0", "note": "MS Annika for cleavable crosslink identification from MS2 spectra", "metadata": { "title": "MS Annika: A New Cross-Linking Search Engine", "abstract": "", "date": "2021-05-07T00:00:00Z", "citationCount": 22, "authors": [], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.3c00325", "pmid": "37566781", "pmcid": "PMC10476269", "type": [ "Primary" ], "version": "2.0", "note": "MS Annika 2.0 for cleavable crosslink identification from MS3 spectra", "metadata": { "title": "MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity", "abstract": "", "date": "2023-09-01T00:00:00Z", "citationCount": 5, "authors": [], "journal": "Journal of Proteome Research" } }, { "doi": "10.1038/s42004-024-01386-x", "pmid": "39702463", "pmcid": "PMC11659399", "type": [ "Primary" ], "version": "3.0", "note": "MS Annika 3.0 for non-cleavable crosslink identification", "metadata": { "title": "Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex", "abstract": "", "date": "2024-12-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Communications Chemistry" } } ], "credit": [ { "name": "Viktoria Dorfer", "email": "viktoria.dorfer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0000-0002-5332-5701", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Micha Birklbauer", "email": "micha.birklbauer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0009-0005-1051-179X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "michabirklbauer", "additionDate": "2023-07-26T14:40:01.768324Z", "lastUpdate": "2025-10-26T02:38:48.643054Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "celltypist", "description": "A tool for semi-automatic cell type classification", "homepage": "https://github.com/Teichlab/celltypist", "biotoolsID": "celltypist", "biotoolsCURIE": "biotools:celltypist", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2025-10-25T16:55:18.980477Z", "lastUpdate": "2025-10-25T16:55:18.983464Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SHAMAN", "description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].", "homepage": "http://shaman.c3bi.pasteur.fr/", "biotoolsID": "shaman", "biotoolsCURIE": "biotools:shaman", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" }, { "uri": "http://edamontology.org/operation_3221", "term": "Species frequency estimation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": "Quantitative metagenomics Count table & taxonomy Diversity, barplot, boxplot, scatterplot, rarefaction curves, heatmap", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/aghozlane/shaman", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://shaman.c3bi.pasteur.fr/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1073/pnas.1523899113", "pmid": "27140611", "pmcid": "PMC4878514", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection", "abstract": "Listeria monocytogenes is responsible for gastroenteritis in healthy individuals and for a severe invasive disease in immunocompromised patients. Among the three identified L. monocytogenes evolutionary lineages, lineage I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms underlying the higher virulence potential of strains of this lineage remain elusive. Here, we demonstrate that Listeriolysin S (LLS), a virulence factor only present in a subset of lineage I strains, is a bacteriocin highly expressed in the intestine of orally infected mice that alters the host intestinal microbiota and promotes intestinal colonization by L. monocytogenes, as well as deeper organ infection. To our knowledge, these results therefore identify LLS as the first bacteriocin described in L. monocytogenes and associate modulation of host microbiota by L. monocytogenes epidemic strains to increased virulence.", "date": "2016-05-17T00:00:00Z", "citationCount": 87, "authors": [ { "name": "Quereda J.J." }, { "name": "Dussurget O." }, { "name": "Nahori M.-A." }, { "name": "Ghozlane A." }, { "name": "Volant S." }, { "name": "Dillies M.-A." }, { "name": "Regnault B." }, { "name": "Kennedy S." }, { "name": "Mondot S." }, { "name": "Villoing B." }, { "name": "Cossart P." }, { "name": "Pizarro-Cerda J." } ], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } } ], "credit": [ { "name": "Stevenn Volant", "email": null, "url": "https://research.pasteur.fr/en/member/stevenn-volant/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Hugo Varet", "email": null, "url": "https://research.pasteur.fr/en/member/hugo-varet/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pierre Lechat", "email": null, "url": "https://research.pasteur.fr/en/member/pierre-lechat/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Amine Ghozlane", "email": null, "url": "https://research.pasteur.fr/en/member/amine-ghozlane/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Institut Pasteur", "email": null, "url": "https://research.pasteur.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "C3BI", "email": null, "url": "https://research.pasteur.fr/en/center/c3bi/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics Hub", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "SHAMAN team", "email": "shaman@pasteur.fr", "url": "https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aghozlane", "additionDate": "2016-11-28T10:07:16Z", "lastUpdate": "2025-10-23T10:46:59.953305Z", "editPermission": { "type": "group", "authors": [ "hmenager", "khillion", "vashokan" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ViVo Platform", "description": "ViVo Platform is a free, open-access web application for the analysis of in vivo tumor growth data in mouse models.\nDesigned to standardize in vivo efficacy analysis, improve research reproducibility, and reduce animal usage, it provides tools to upload tumor volume or bioluminescence imaging (BLI) datasets, configure analysis parameters, detect outliers, and automatically compute tumor growth rates (TGR), group comparisons, and reports.\n\nBy standardizing data processing and incorporating advanced temporal modeling, ViVo Platform enhances statistical power and contributes to the 3Rs principle by reducing the number of animals needed in preclinical efficacy studies.", "homepage": "https://gcanudo-barreras.github.io/ViVo-Platform/", "biotoolsID": "vivo_platform", "biotoolsCURIE": "biotools:vivo_platform", "version": [ "Research Beta 1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Data analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3722", "term": "Physiology parameter" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3723", "term": "Morphology parameter" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3386", "term": "Laboratory animal science" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [ "JavaScript" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gcanudo-barreras.github.io/ViVo-Platform/", "type": [ "Service" ], "note": null }, { "url": "https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1", "type": [ "Other" ], "note": "bioRxiv preprint" }, { "url": "https://github.com/gcanudo-barreras/ViVo-Platform", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/ViVo_USER_MANUAL.md", "type": [ "User manual" ], "note": null }, { "url": "https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1", "type": [ "Other" ], "note": "Full methodology" }, { "url": "https://github.com/gcanudo-barreras/ViVo-Platform/releases/tag/v1.0-beta", "type": [ "Release notes" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.10.14.682266", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": "Research Beta 1.0", "note": null, "metadata": null } ], "credit": [ { "name": "Guillermo Canudo-Barreras", "email": "canudobarreras@unizar.es", "url": null, "orcidid": "https://orcid.org/0000-0002-1949-9185", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Maintainer", "Support" ], "note": "Researcher at Spanish National Research Council (CSIC). Developer." }, { "name": "Eduardo Romanos", "email": "eromanos.iacs@aragon.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9918-3374", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Researcher at Biomedical Research Center of Aragon (CIBA)." }, { "name": "Raquel P. Herrera", "email": "raquelph@unizar.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5244-9569", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Senior scientist at Spanish National Research Council (CSIC)." }, { "name": "M. Concepción Gimeno", "email": "gimeno@unizar.es", "url": null, "orcidid": "https://orcid.org/0000-0003-0553-0695", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Full professor at Spanish National Research Council (CSIC)." } ], "owner": "gcanudo-barreras", "additionDate": "2025-10-23T09:01:44.958137Z", "lastUpdate": "2025-10-23T09:09:29.560348Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SuShiE", "description": "Software to perform multi-ancestry SNP fine-mapping on molecular data", "homepage": "https://github.com/mancusolab/sushie", "biotoolsID": "sushie", "biotoolsCURIE": "biotools:sushie", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2025-10-22T22:25:09.138227Z", "lastUpdate": "2025-10-22T22:25:09.140568Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EAPP - Extended a Priori Probability tool", "description": "The tool provides a semi-supervised metric (EAPP) for binary classification tasks that considers not only the a priori probability but also some possible bias present in the dataset, as well as other features that could provide a relatively trivial separability of the target classes. Therefore, it allows for evaluating the ease or complexity of the task or bias of the data beyond the well-established baseline for any binary classification.", "homepage": "https://ieeexplore.ieee.org/document/9950248", "biotoolsID": "extended_a_priori_probability_tool", "biotoolsCURIE": "biotools:extended_a_priori_probability_tool", "version": [ "v1.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Data analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [], "language": [], "license": "Proprietary", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/1Kym-bIgDULo5fZMsDQC2dOGW_o1Lnw4x/edit?usp=drive_link&ouid=104810445060833398927&rtpof=true&sd=true", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1109/ACCESS.2022.3221936", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Extended a Priori Probability (EAPP): A Data-Driven Approach for Machine Learning Binary Classification Tasks", "abstract": "", "date": "2022-01-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "IEEE Access" } } ], "credit": [], "owner": "dsilveira", "additionDate": "2025-05-22T14:58:20.772120Z", "lastUpdate": "2025-10-22T15:38:34.323925Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Image Quality Assessment metrics (IQA) for XNAT platform", "description": "Docker images developped at the Euro-BioImaging MED-Hub and National Research Council (CNR) for the XNAT platform hosted by University of Turin. A suite of four Image Quality Assessment (IQA) metrics designed to evaluate the perceptual quality of clinical image datasets within the XNAT platform at the scan and subject levels. The tool outputs Excel files containing the mean and median for each metric and scan, as well as PNG files with corresponding histogram plots.", "homepage": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "biotoolsID": "image_quality_assessment_metrics_iqa_for_xnat_platform", "biotoolsCURIE": "biotools:image_quality_assessment_metrics_iqa_for_xnat_platform", "version": [], "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_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [], "operatingSystem": [], "language": [ "MATLAB", "Python" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/17goRA76d9vViR93HbhIcjPPxsCdtGhS9/edit?usp=sharing&ouid=114076787312989347088&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "Feriel", "additionDate": "2025-10-15T07:25:34.085350Z", "lastUpdate": "2025-10-22T13:44:38.894557Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NLmCED Filter", "description": "The NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination between two filters such as the Non-Local mean filter and the Anisotropic Diffusion tensor method with an estimator of Rician noise. The NLmCED filter can benefit from the noise reduction capabilities of the NLM filter while maintaining the edge-preserving characteristics of anisotropic diffusion.", "homepage": "https://github.com/Feriel87/Denoising-CEST-MRI/tree/main/NLmCED_Filter", "biotoolsID": "nlmced_filter", "biotoolsCURIE": "biotools:nlmced_filter", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "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 } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [], "language": [ "Python", "MATLAB" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FerielRamdhane/Denoising-CEST-MRI/tree/main/NLmCED_Filter", "type": [ "Repository" ], "note": "Github Link" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1504/IJCVR.2018.090012", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A new method for three-dimensional magnetic resonance images denoising", "abstract": "", "date": "2018-01-01T00:00:00Z", "citationCount": 3, "authors": [], "journal": "International Journal of Computational Vision and Robotics" } } ], "credit": [], "owner": "Feriel", "additionDate": "2023-07-13T08:14:40.190855Z", "lastUpdate": "2025-10-22T13:34:04.781714Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)", "description": "A customisable image pre-processing tool that performs 5 of the most common denoising filters and ANTS N4 bias field correction filter.", "homepage": "https://www.acim.lafe.san.gva.es/acim/?page_id=675&lang=es", "biotoolsID": "denoising-inhomogeneity_correction_tool", "biotoolsCURIE": "biotools:denoising-inhomogeneity_correction_tool", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" } ], "operatingSystem": [], "language": [], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.google.com/file/d/1W0aHAIG_bdU9Z1J3aDNsb1r39WBuX9Ot/view?usp=drive_link", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s10278-021-00512-8", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MR Denoising Increases Radiomic Biomarker Precision and Reproducibility in Oncologic Imaging", "abstract": "", "date": "2021-10-01T00:00:00Z", "citationCount": 12, "authors": [], "journal": "Journal of Digital Imaging" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T08:55:46.088021Z", "lastUpdate": "2025-10-22T11:13:35.505154Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Integration of multiple datasets", "description": "Collection and integration of multiple datasets with all pre-existing health and environmental data relevant to REMEDIA’s research objectives from the participating cohorts and registries.", "homepage": "https://h2020-remedia.eu/toolbox/integration-of-multiple-datasets", "biotoolsID": "integration_of_multiple_datasets", "biotoolsCURIE": "biotools:integration_of_multiple_datasets", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "Sophynet", "additionDate": "2025-10-22T10:30:16.042916Z", "lastUpdate": "2025-10-22T10:30:16.045372Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)", "description": "The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files.\n\nStatus : Containerized", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "biotoolsID": "dicom_file_integrity_checker_by_gibi230", "biotoolsCURIE": "biotools:dicom_file_integrity_checker_by_gibi230", "version": [ "1.2.9", "2.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.google.com/file/d/1s8-nVAvSuAGTHWwun4AQcgHtRWclsFg2/view?usp=sharing", "type": [ "General" ], "note": "Pedro-Miguel Martinez-Girones 1,*, Adrian Galiana-Bordera 1, Carina Soler-Pons 1, Ignacio Gomez-Rico-Junquero 1, Ignacio Blanquer-Espert 3, Leonor Cerda-Alberich 1 and Luis Marti-Bonmati 1,2\n1\tBiomedical Imaging Research Group (GIBI230), La Fe Health Research Institute (IIS La Fe), Avenida Fernando Abril Martorell, València, 46026, Spain.\n2\tLa Fe Medical Imaging Department, Avenida Fernando Abril Martorell, València, 46026, Spain.\n3\tComputing Science Department, Universitat Politècnica de València, Cami de Vera s/n, València, 46022, Spain." } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2025-10-22T10:24:29.224315Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "nf-core-proteinfamilies", "description": "nf-core/proteinfamilies is a bioinformatics pipeline that generates protein families from amino acid sequences and/or updates existing families with new sequences. It takes a protein fasta file as input, clusters the sequences and then generates protein family Hiden Markov Models (HMMs) along with their multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs and MSAs can be given (must have matching base filenames one-to-one) in order to update with new sequences in case of matching hits.", "homepage": "https://github.com/nf-core/proteinfamilies", "biotoolsID": "nf-core_proteinfamilies", "biotoolsCURIE": "biotools:nf-core_proteinfamilies", "version": [ "2.0.0" ], "otherID": [ { "value": "RRID:SCR_027374", "type": "rrid", "version": "1.3.0" } ], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [], "language": [ "Groovy" ], "license": "MIT", "collectionID": [ "nf-core" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/nf-core/proteinfamilies", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2025.08.12.670010", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "vangelis", "additionDate": "2025-09-22T13:08:24.320192Z", "lastUpdate": "2025-10-22T08:47:05.530398Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gentropy", "description": "Open Targets python framework for post-GWAS analysis", "homepage": "https://github.com/opentargets/gentropy", "biotoolsID": "gentropy", "biotoolsCURIE": "biotools:gentropy", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2025-10-21T13:58:14.083637Z", "lastUpdate": "2025-10-21T13:58:14.086135Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DDGWizard", "description": "DDGWizard is a ∆∆G analysis system, which includes a feature calculation pipeline that integrates 12 computational resources and is capable\nof automatically calculating 1,547 features for ∆∆G data. The calculated features provide information for the ∆∆G prediction from various perspectives, including the structure and environment of wild-type proteins, structural and environmental changes before and after mutation, mutation types, and evolutionary information. In addition, it provides a feature enriched dataset created using the pipeline, including 15,752 ∆∆G data. Furthermore, it incorporates an accurate ∆∆G prediction model developed with the selected optimal features. The model achieved an R-squared of 0.61 in cross-validation.", "homepage": "https://github.com/bioinfbrad/DDGWizard", "biotoolsID": "ddgwizard", "biotoolsCURIE": "biotools:ddgwizard", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "mingkai", "additionDate": "2025-10-20T18:45:07.801030Z", "lastUpdate": "2025-10-21T08:31:14.927713Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "scDenorm", "description": "scDenorm is a tool that reverts normalised single-cell omics data to raw counts, preserving the integrity of the original measurements and ensuring consistent data processing during integration.", "homepage": "https://pypi.org/project/scDenorm/", "biotoolsID": "scdenorm", "biotoolsCURIE": "biotools:scdenorm", "version": [ "1.0.1" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "changebio", "additionDate": "2025-10-21T04:21:05.804086Z", "lastUpdate": "2025-10-21T04:21:05.806039Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Breast Dense Tissue Segmentation", "description": "The tool takes a digital mammogram and performs an automatic segmentation of the breast area and the dense tissue. After the mammogram segmentation, the tool returns a DICOM-SEG image with both the dense tissue and the breast tissue mask combined.", "homepage": "https://pubmed.ncbi.nlm.nih.gov/36010173/", "biotoolsID": "breast_dense_tissue_segmentation", "biotoolsCURIE": "biotools:breast_dense_tissue_segmentation", "version": [ "v1.0.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Proprietary", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.3390/diagnostics12081822", "pmid": "36010173", "pmcid": "PMC9406546", "type": [], "version": null, "note": null, "metadata": { "title": "Breast Dense Tissue Segmentation with Noisy Labels: A Hybrid Threshold-Based and Mask-Based Approach", "abstract": "", "date": "2022-08-01T00:00:00Z", "citationCount": 7, "authors": [], "journal": "Diagnostics" } } ], "credit": [], "owner": "dsilveira", "additionDate": "2025-05-22T12:06:46.866961Z", "lastUpdate": "2025-10-20T10:26:42.806388Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AfexCore", "description": "AfexCore brings 12 essential bioinformatics tools into one intuitive GUI - built for researchers who need quick, reliable sequence analysis without the complexity (or price tag) of enterprise software.", "homepage": "https://afexgenesis.netlify.app", "biotoolsID": "afexcore", "biotoolsCURIE": "biotools:afexcore", "version": [ "Beta 2.1.4" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "AGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/AfexGenesis/AfexCore", "type": [ "Repository" ], "note": "Official Github Repository of the Software" }, { "url": "https://afexgenesis.netlify.app", "type": [ "Service" ], "note": "Official Website of the Software/Organization" } ], "download": [ { "url": "https://github.com/AfexGenesis/AfexCore/releases/tag/v2.1.4", "type": "Software package", "note": null, "version": "AfexCore 2.1.4 Beta Release" } ], "documentation": [], "publication": [], "credit": [ { "name": "Nirmal Weerapperuma", "email": "afexgenesis@gmail.com", "url": "https://www.instagram.com/nipun_weerapperuma", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "i'm the guy :)" } ], "owner": "AnimateAI", "additionDate": "2025-10-20T03:29:21.364200Z", "lastUpdate": "2025-10-20T03:29:21.366577Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ccbr_tools", "description": "Utilities for CCBR Bioinformatics Software", "homepage": "https://ccbr.github.io/Tools", "biotoolsID": "ccbr_tools", "biotoolsCURIE": "biotools:ccbr_tools", "version": [ "0.4.4" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CCBR/Tools", "type": [ "Repository" ], "note": "link to the documentation website" } ], "download": [], "documentation": [ { "url": "https://ccbr.github.io/Tools", "type": [ "API documentation" ], "note": null } ], "publication": [], "credit": [], "owner": "kelly-sovacool", "additionDate": "2025-10-17T20:41:51.279787Z", "lastUpdate": "2025-10-17T20:47:15.160556Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Data Integration Quality Check Tool (DIQCT)", "description": "The Tool performs a quality assessment of a dataset based on a series of requirements that are set specifically for each use case. The tool informs the user of corrective actions that need to be taken prior to the data provision to ensure that the data provided is of high quality and reports a series of quality metrics characterizing the specific dataset.", "homepage": "https://www.mdpi.com/2939712", "biotoolsID": "data_integration_quality_check_tool_diqct", "biotoolsCURIE": "biotools:data_integration_quality_check_tool_diqct", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "R", "Python" ], "license": "Proprietary", "collectionID": [ "eucaim" ], "maturity": "Mature", "cost": "Commercial", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/1b_5-pf94_QeOZVT2wVdG1YpWkAiTskwa/edit?usp=sharing&ouid=106267739460923945711&rtpof=true&sd=true", "type": [ "Other" ], "note": null }, { "url": "https://docs.google.com/document/d/1EnkkmFOGAo-WhPwx3OQ8vxSb3FKFn4b-/edit?usp=sharing&ouid=106267739460923945711&rtpof=true&sd=true", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.3390/info15090533", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Toward Ensuring Data Quality in Multi-Site Cancer Imaging Repositories", "abstract": "", "date": "2024-09-01T00:00:00Z", "citationCount": 3, "authors": [], "journal": "Information (Switzerland)" } }, { "doi": "10.1109/EMBC48229.2022.9871018", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Data Quality Check in Cancer Imaging Research: Deploying and Evaluating the DIQCT Tool", "abstract": "", "date": "2022-01-01T00:00:00Z", "citationCount": 4, "authors": [], "journal": "Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS" } } ], "credit": [ { "name": "Ioanna Chouvarda", "email": "ioannach@auth.gr", "url": null, "orcidid": "https://orcid.org/0000-0001-8915-6658", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "authEucaim", "additionDate": "2025-05-16T09:56:39.880752Z", "lastUpdate": "2025-10-17T07:24:02.533259Z", "editPermission": { "type": "group", "authors": [ "dimfilos" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Tabular Data Curator", "description": "A fully automated service which can be applied on any kind of tabular data (e.g. clinical) to automatically identify duplicated fields (lexically similar and/or highly correlated features), outliers, data inconsistencies. It can also deal with missing values through the application of data imputers.", "homepage": "https://github.com/vpz4/TDC", "biotoolsID": "tabular_data_curator", "biotoolsCURIE": "biotools:tabular_data_curator", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [], "language": [ "Python" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/vpz4/TDC", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/vpz4/TDC", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1016/j.compbiomed.2019.03.001", "pmid": "30878889", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Medical data quality assessment: On the development of an automated framework for medical data curation", "abstract": "", "date": "2019-04-01T00:00:00Z", "citationCount": 85, "authors": [], "journal": "Computers in Biology and Medicine" } } ], "credit": [], "owner": "bpezoulas", "additionDate": "2025-10-15T12:28:27.006057Z", "lastUpdate": "2025-10-15T12:39:18.021382Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "raw2ometiff", "description": "Raw format to OME-TIFF converter", "homepage": "https://github.com/glencoesoftware/raw2ometiff", "biotoolsID": "raw2ometiff", "biotoolsCURIE": "biotools:raw2ometiff", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2025-10-14T20:17:27.875866Z", "lastUpdate": "2025-10-14T20:17:27.879215Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bioformats2raw", "description": "Bio-Formats image file format to raw format converter", "homepage": "https://github.com/glencoesoftware/bioformats2raw", "biotoolsID": "bioformats2raw", "biotoolsCURIE": "biotools:bioformats2raw", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2025-10-14T20:16:50.609208Z", "lastUpdate": "2025-10-14T20:16:50.611768Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Dynamont", "description": "A Dynamic Programming Approach to Segment ONT Signals. Dynamont is a segmentation/resquiggling tool for ONT signals.", "homepage": "https://github.com/rnajena/dynamont", "biotoolsID": "dynamont", "biotoolsCURIE": "biotools:dynamont", "version": [ "0.7.2" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "Jannes", "additionDate": "2025-10-14T12:23:40.079667Z", "lastUpdate": "2025-10-14T12:27:29.187590Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "QP-Insights Uploader", "description": "This desktop application enables users to upload DICOM data along with associated clinical information to QP-Insights—the data management platform of the UPV Reference Node within EUCAIM.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/qp_insights_uploader/artifacts-tab", "biotoolsID": "qp-insights_uploader", "biotoolsCURIE": "biotools:qp-insights_uploader", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_0956", "term": "Data index report" }, "format": [ { "uri": "http://edamontology.org/format_3580", "term": "rcc" }, { "uri": "http://edamontology.org/format_3468", "term": "xls" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" } ], "operatingSystem": [ "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/qp_insights_uploader/artifacts-tab", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://eucaim.gitbook.io/enduserguide/6-userguide4members", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Quibim", "email": null, "url": "https://quibim.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "celia_martin", "additionDate": "2025-05-21T12:27:35.032026Z", "lastUpdate": "2025-10-14T09:57:32.885338Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TNMplot", "description": "TNMplot.com is a free, interactive web tool for comparing gene expression in normal, tumor, and metastatic tissues across over 56,900 samples (TCGA, GTEx, GEO). It supports pan-cancer and tissue-specific analysis, offering boxplots, violin plots, sensitivity–specificity curves, and stage-specific comparisons.", "homepage": "http://www.tnmplot.com", "biotoolsID": "tnmplot", "biotoolsCURIE": "biotools:tnmplot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0315", "term": "Expression profile comparison" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_3360", "term": "Biomarkers" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.3390/IJMS22052622", "pmid": "33807717", "pmcid": "PMC7961455", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Tnmplot.Com: A web tool for the comparison of gene expression in normal, tumor and metastatic tissues", "abstract": "", "date": "2021-03-01T00:00:00Z", "citationCount": 688, "authors": [], "journal": "International Journal of Molecular Sciences" } } ], "credit": [ { "name": "Balázs Győrffy", "email": "gyorffy.balazs@med.semmelweis-univ.hu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Áron Bartha", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "zsmag19", "additionDate": "2021-01-18T11:58:25Z", "lastUpdate": "2025-10-14T09:17:21.842269Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "cancer hallmarks", "description": "CancerHallmarks.com is an interactive web tool that analyzes gene lists based on the ten canonical hallmarks of cancer. It integrates 6,763 hallmark-associated genes (core set: 1,574) from multiple databases and offers enrichment analysis with clear bar and distribution plots.", "homepage": "https://cancerhallmarks.com/", "biotoolsID": "cancer_hallmarks", "biotoolsCURIE": "biotools:cancer_hallmarks", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "bioinformatika", "additionDate": "2025-07-10T07:25:58.694382Z", "lastUpdate": "2025-10-14T09:07:47.406337Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cells2visium", "description": "segmenting H&E images from Visium to assign each visium spot to the number of cell, occupancy and other morphological features of cells", "homepage": "https://github.com/cellgeni/cells2visium", "biotoolsID": "cells2visium", "biotoolsCURIE": "biotools:cells2visium", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2025-09-23T15:11:59.204153Z", "lastUpdate": "2025-10-14T09:04:03.542177Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bin2cell", "description": "Join subcellular Visium HD bins into cells.", "homepage": "https://github.com/Teichlab/bin2cell", "biotoolsID": "bin2cell", "biotoolsCURIE": "biotools:bin2cell", "version": [ "0.3.3" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btae546", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Bin2cell reconstructs cells from high resolution Visium HD data", "abstract": "", "date": "2024-09-01T00:00:00Z", "citationCount": 21, "authors": [], "journal": "Bioinformatics" } } ], "credit": [], "owner": "camlloyd", "additionDate": "2025-09-23T15:10:25.737722Z", "lastUpdate": "2025-10-14T09:02:29.580064Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "exposomeShiny", "description": "ExposomeShiny is a standalone web application implemented in R. It is available as source files and can be installed in any server or computer avoiding problems with data confidentiality. It is executed in RStudio which opens a browser window with the web application and provides a bridge between researchers and most of the state-of-the-art exposome analysis methodologies, without the need for advanced programming skills.", "homepage": "https://github.com/isglobal-brge/exposomeShiny/tree/master", "biotoolsID": "exposomeshiny_-_a_toolbox_for_exposome_data_analysis", "biotoolsCURIE": "biotools:exposomeshiny_-_a_toolbox_for_exposome_data_analysis", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://isglobal-brge.github.io/exposome_bookdown/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/ije/dyab220", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Software Application Profile: ExposomeShiny - A toolbox for exposome data analysis", "abstract": "", "date": "2022-02-01T00:00:00Z", "citationCount": 3, "authors": [], "journal": "International Journal of Epidemiology" } } ], "credit": [], "owner": "rodney", "additionDate": "2025-10-07T12:12:24.732038Z", "lastUpdate": "2025-10-14T07:53:00.001965Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "We-expose", "description": "The WE-EXPOSE (Working Life Exposome for Policy, OSH and Science) Toolbox makes available tools developed in the EU EPHOR project for different stakeholders focused on: innovative methods and improved knowledge.", "homepage": "https://www.we-expose.eu/", "biotoolsID": "we-expose", "biotoolsCURIE": "biotools:we-expose", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3855", "term": "Environmental sciences" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" }, { "uri": "http://edamontology.org/topic_4010", "term": "Open science" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "EHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "eelco", "additionDate": "2025-04-17T13:14:18.531116Z", "lastUpdate": "2025-10-13T08:20:43.268568Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Equal-Life Toolbox Collection", "description": "Web-based toolbox of the Equal-Life project. With the tools gallery and a comprehensive interactive guidebook.", "homepage": "https://www.equal-life-toolbox.eu/", "biotoolsID": "equal-life_toolbox_collection", "biotoolsCURIE": "biotools:equal-life_toolbox_collection", "version": [], "otherID": [], "relation": [ { "biotoolsID": "rexposome", "type": "includes" } ], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Anna Sandionigi", "email": "anna.sandionigi@quantiaconsulting.com", "url": null, "orcidid": "https://orcid.org/0000-0002-5257-0027", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Equal-Life Toolbox developer" } ], "owner": "annasandionigi", "additionDate": "2025-10-13T07:29:45.909943Z", "lastUpdate": "2025-10-13T07:30:02.656269Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PolySTest", "description": "Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.", "homepage": "http://computproteomics.bmb.sdu.dk/Apps/PolySTest", "biotoolsID": "PolySTest", "biotoolsCURIE": "biotools:PolySTest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "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_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3932", "term": "Q-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_3905", "term": "Histogram" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Denmark" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/computproteomics/PolySTest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1074/mcp.RA119.001777", "pmid": "32424025", "pmcid": "PMC8015005", "type": [], "version": null, "note": null, "metadata": { "title": "PolySTest: Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features", "abstract": "", "date": "2020-08-01T00:00:00Z", "citationCount": 23, "authors": [], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [], "owner": "veits@bmb.sdu.dk", "additionDate": "2019-11-14T19:27:27Z", "lastUpdate": "2025-10-10T08:22:56.998896Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "html4blast", "description": "Create a html report from a blast result.", "homepage": "https://bioweb.pasteur.fr/packages/pack@html4blast@1.7a", "biotoolsID": "html4blast", "biotoolsCURIE": "biotools:html4blast", "version": [ "1.7a" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BLAST utility", "galaxyPasteur", "Institut Pasteur" ], "maturity": "Legacy", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/mblastall/html4blast/1.7a", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "", "date": "2016-07-08T00:00:00Z", "citationCount": 1483, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:22:32Z", "lastUpdate": "2025-10-09T12:11:39.700640Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "oncoanalyser", "description": "Oncoanalyser is an nf-core Nextflow implementation of the tools developed by Hartwig Medical Foundation. The workflow is designed to comprehensively detect all variant types (SNV. MNV, InDel, SV, CNV, Fusions, Viral insertions, Telomere length, Genetic Immune Escape, mutational processes) as well as key tumor characteristics (purity, ploidy, TMB, MSI) from data derived from different short read platforms. The tooling is optimised for paired whole genome samples (90x tumor, 30x normal) but can be run on exome or panel (targeted) data. There is support for GRCh37 and GRCh38 human reference genome builds.", "homepage": "https://github.com/nf-core/oncoanalyser/tree/dev", "biotoolsID": "oncoanalyser", "biotoolsCURIE": "biotools:oncoanalyser", "version": [ "5.34" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/nf-core/oncoanalyser/tree/dev", "type": [ "Issue tracker", "Repository" ], "note": "GitHub page for issue tracking of Nextflow workflow implementation" }, { "url": "https://github.com/hartwigmedical/hmftools", "type": [ "Repository", "Issue tracker" ], "note": "GitHub repository of underlying tools with issue tracking" } ], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "jdeligt", "additionDate": "2024-03-07T20:51:08.529472Z", "lastUpdate": "2025-10-09T07:39:49.943872Z", "editPermission": { "type": "group", "authors": [ "jdeligt", "VKasalica" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "miRTARGET", "description": "miRTARGET is an integrated web tool for the identification of microRNA targets with potential therapeutic or prognostic value in cancer. The target prediction is based on four dataset categories: mRNA profiling in cells or mice after (1) ectopic miRNA expression or (2) miRNA inactivation by knock-out or knock-down, (3) correlation analyses of mRNA and miRNA expression profiles, and (4) ten computational miRNA target prediction algorithms.", "homepage": "https://www.mirtarget.com/", "biotoolsID": "mirtarget", "biotoolsCURIE": "biotools:mirtarget", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "Matjaz1976", "additionDate": "2025-10-08T12:52:22.479733Z", "lastUpdate": "2025-10-08T12:52:22.481900Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "datmat", "description": "‘datmat’ is a Python package aimed to easily gather data from a variety of sources and materialize it into a standardized format. It can download projects of imaging data from XNAT into the EUCAIM folder structure, and is designed to be extendible to support other inputs and outputs.", "homepage": "https://gitlab.com/radiology/infrastructure/data-materialisation/", "biotoolsID": "datmat", "biotoolsCURIE": "biotools:datmat", "version": [ "0.2.0" ], "otherID": [], "relation": [ { "biotoolsID": "xnatpy", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Data sorting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://pypi.org/project/datmat/", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/datmat/", "type": "Software package", "note": null, "version": null }, { "url": "https://gitlab.com/radiology/infrastructure/data-materialisation", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://datmat.readthedocs.io/latest/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Alexander Harms", "email": "alexander.harms@health-ri.nl", "url": null, "orcidid": "https://orcid.org/0009-0001-5727-6732", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Hakim Achterberg", "email": "h.achterberg@erasmusmc.nl", "url": null, "orcidid": "https://orcid.org/0000-0003-3772-4582", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Erasmus MC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "018906e22", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "agjharms", "additionDate": "2025-08-25T14:36:13.568250Z", "lastUpdate": "2025-10-07T13:06:50.742010Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "img2catalog", "description": "This tool, 'img2catalog', is built to extract metadata from imaging data repositories, map it to a model class, and export it to a catalog. The tool is set up to be modular, but it currently supports extracting metadata from an XNAT server, converting it to the Health-RI Core v2 metadata model (https://github.com/Health-RI/health-ri-metadata/tree/v2.0.0) based on DCAT-AP v3 and Health-DCAT AP, as defined in Pydantic classes using SeMPyRO (https://github.com/Health-RI/SeMPyRO) and either writing it to an RDF file, or pushing it to a FAIR Data Point (FDP).", "homepage": "https://github.com/Health-RI/img2catalog", "biotoolsID": "img2catalog", "biotoolsCURIE": "biotools:img2catalog", "version": [ "1.0.1" ], "otherID": [], "relation": [ { "biotoolsID": "xnatpy", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Data parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Health-RI/img2catalog", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/Health-RI/img2catalog", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/img2catalog/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/Health-RI/img2catalog/blob/main/README.md", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Alexander Harms", "email": "alexander.harms@health-ri.nl", "url": null, "orcidid": "https://orcid.org/0009-0001-5727-6732", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Health-RI", "email": null, "url": "https://www.health-ri.nl/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "agjharms", "additionDate": "2025-08-25T14:46:01.217831Z", "lastUpdate": "2025-10-07T13:06:17.716157Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Health-RI XNAT", "description": "Imaging platform for multi-centre clinical studies, hosted by Health-RI. The platform is based on the open source XNAT software and the RSNA CTP software.", "homepage": "https://xnat.health-ri.nl", "biotoolsID": "xnat.bmia.nl", "biotoolsCURIE": "biotools:xnat.bmia.nl", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" }, { "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_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_3546", "term": "Image metadata" }, "format": [ { "uri": "http://edamontology.org/format_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "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_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_3546", "term": "Image metadata" }, "format": [ { "uri": "http://edamontology.org/format_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BioMedBridges Tools", "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.healthdata.nl/health-ri-servicedesk", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "https://xnat.health-ri.nl/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Health-RI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "BioMedBridges", "email": null, "url": "http://www.biomedbridges.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Documentor" ], "note": null }, { "name": "Stefan Klein", "email": "s.klein@erasmusmc.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hachterberg", "additionDate": "2015-02-04T09:14:45Z", "lastUpdate": "2025-10-07T12:17:41.033029Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Plausibility database", "description": "This plausibility database summarises the level of evidence regarding the effects of environmental hazards (chemical and urban) linking the exposome’s effect on children’s health. This assessment of evidence levels can synthesise findings across many exposure factors and outcomes, identify understudied domains in children’s environmental health, highlight emerging concerns, or help perform health impact assessment studies.\n\nMore information about the approach that was developed to extract and summarise the existing evidence about effects of environmental factors on health, is available in a publication by Colzin S et al. (2024).The plausibility database is available in a downloadable table.", "homepage": "https://athleteproject.eu/download/1987/?tmstv=1736854726", "biotoolsID": "plausibility_database", "biotoolsCURIE": "biotools:plausibility_database", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "rodney", "additionDate": "2025-10-07T12:16:07.372519Z", "lastUpdate": "2025-10-07T12:17:05.650534Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Catalogue - Blood eQTMs in children", "description": "Web application to download correlations between DNA methylation and expression of nearby genes (eQTMs) in child blood. It will help biological interpretation of epigenome-wide association studies (EWAS) in children.", "homepage": "https://helixomics.isglobal.org/", "biotoolsID": "catalogue_-_blood_eqtms_in_children", "biotoolsCURIE": "biotools:catalogue_-_blood_eqtms_in_children", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "rodney", "additionDate": "2025-10-07T12:15:22.246139Z", "lastUpdate": "2025-10-07T12:15:22.248293Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HELIX cohort", "description": "The Human Early Life Exposome (HELIX) cohort study gathers longitudinal population-based birth cohort data from six European countries. It includes biomarkers, omics signatures, and health outcomes. Researchers can get access to this data upon request.", "homepage": "https://athleteproject.eu/helix-cohort/", "biotoolsID": "helix_cohort", "biotoolsCURIE": "biotools:helix_cohort", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "rodney", "additionDate": "2025-10-07T11:51:50.476512Z", "lastUpdate": "2025-10-07T11:53:16.172930Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }