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{ "count": 30644, "next": "?page=2", "previous": null, "list": [ { "name": "seqfu", "description": "A collection of utilities to manipulate FASTA and FASTQ files, supporting Gzipped input.", "homepage": "https://telatin.github.io/seqfu2/", "biotoolsID": "seqfu", "biotoolsCURIE": "biotools:seqfu", "version": [ "1.10.0", "1.11.0", "1.12.0", "1.13.0", "1.14.0", "1.15.0", "1.16.0", "1.17.0", "1.19.0", "1.20.0", "1.21.0", "1.22.0", "1.22.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [] } ], "note": null, "cmd": "seqfu [subcommand] FASTX > FASTX" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://telatin.github.io/seqfu2", "type": [ "Other" ], "note": "Documentation" }, { "url": "https://github.com/telatin/seqfu2/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/telatin/seqfu2", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/telatin/seqfu2/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://bioconda.github.io/recipes/seqfu/README.html", "type": "Software package", "note": null, "version": "1.0.0-1.22.3" } ], "documentation": [ { "url": "https://telatin.github.io/seqfu2/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.3390/bioengineering8050059", "pmid": "34066939", "pmcid": "PMC8148589", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "Seqfu: A suite of utilities for the robust and reproducible manipulation of sequence files", "abstract": "", "date": "2021-01-01T00:00:00Z", "citationCount": 36, "authors": [], "journal": "Bioengineering" } } ], "credit": [], "owner": "telatin", "additionDate": "2020-03-17T13:50:50Z", "lastUpdate": "2025-12-12T21:43:34.328705Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)", "description": "The tool performs an automatic segmentation of the possible glioblastoma tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core), edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region), total (Total tumor including edema and necrosis by a single model) and total-fused (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing steps as skull stripping, intra-patient registration, z-score normalization, patching, among others. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_glioblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_glioblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-selector /input/config/series.csv \\\n --target total \\\n --emit-config true" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-list '[{\"dataset_id\":\"DS001\",\"patient_id\":\"PAT001\",\"study_id\":\"ST001\",\"series_path\":\"/input/DICOM/DS001/PAT001/ST001/T1_POST\"}]' \\\n --target total-fused \\\n --emit-config true" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/s11548-024-03205-z", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Deep learning automatic semantic segmentation of glioblastoma multiforme regions on multimodal magnetic resonance images", "abstract": "", "date": "2024-09-01T00:00:00Z", "citationCount": 8, "authors": [], "journal": "International Journal of Computer Assisted Radiology and Surgery" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Maria Beser-Robles", "email": "maria_beser@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-0072-5525", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Support" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T12:09:16.704255Z", "lastUpdate": "2025-12-12T17:44:52.770153Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)", "description": "This tool is specifically designed and validated for automated detection and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG.\n\nTRAINING & VALIDATION COHORTS:\n\nInitial Development (Veiga-Canuto 2022):\n-Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).\n-Internal validation: 26 patients (median DSC 0.918 ± 0.067).\n-Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).\n-Mean age: 37.6 ± 39.3 months.\n-Median tumor volume: 116,518 mm³.\n\nExternal Validation (Veiga-Canuto 2023):\n-300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).\n-Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.\n-Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12).\n-Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_neuroblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n --gpus all \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \\\n --mode dicom-seg \\\n --series-selector /output/config/series_to_segment.csv \\\n --seg-series-number 2302001 \\\n --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\" \\\n --seg-coordinating-center \"EUCAIM Consortium\" \\\n --keep-nifti false" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "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://www.mdpi.com/2072-6694/14/15/3648", "type": [ "General" ], "note": null }, { "url": "https://drive.google.com/file/d/1xzmrPQx9LfZr6WS5OR80RkipukoO_3Gw/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.3390/cancers14153648", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comparative Multicentric Evaluation of Inter-Observer Variability in Manual and Automatic Segmentation of Neuroblastic Tumors in Magnetic Resonance Images", "abstract": "", "date": "2022-08-01T00:00:00Z", "citationCount": 33, "authors": [], "journal": "Cancers" } }, { "doi": "10.3390/cancers15051622", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Independent Validation of a Deep Learning nnU-Net Tool for Neuroblastoma Detection and Segmentation in MR Images", "abstract": "", "date": "2023-03-01T00:00:00Z", "citationCount": 15, "authors": [], "journal": "Cancers" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T09:08:44.174795Z", "lastUpdate": "2025-12-12T17:33:20.177332Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Annotation Seg Converter", "description": "This repository provides tools for segmentation files conversion in DicomSEG, with a primary focus on: DICOM RTSTRUCT to DICOM SEG: A Python script (rtstruct/rtstruct2dcmseg.py) converts DICOM Radiotherapy Structure Set (RTSTRUCT) files, along with their referenced DICOM image series, into DICOM Segmentation (SEG) objects. It can also optionally convert the individual Regions of Interest (ROIs) defined in the RTSTRUCT into separate NIfTI (.nii.gz) files. Nifti Conversions via dcmqi and Custom Scripts: The Docker image built from this repository also includes command-line tools from dcmqi (DICOM Quantitative Imaging Toolkit) and custom Python scripts for various conversions, such as: ITK image formats (NIfTI, NRRD) to/from DICOM SEG. DICOM series to NIfTI. DICOM SEG to NIfTI (custom alternative).", "homepage": "https://github.com/marver17/DICOMSEG_Converter", "biotoolsID": "dicomseg_converter", "biotoolsCURIE": "biotools:dicomseg_converter", "version": [ "1.4.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/marver17/DICOMSEG_Converter", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/marver17/DICOMSEG_Converter", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1186/s13244-021-01081-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "How does DICOM support big data management? Investigating its use in medical imaging community", "abstract": "", "date": "2021-12-01T00:00:00Z", "citationCount": 34, "authors": [], "journal": "Insights into Imaging" } } ], "credit": [ { "name": "Mario Verdicchio", "email": "mario.verdicchio@synlab.it", "url": null, "orcidid": "https://orcid.org/0000-0002-3762-3100", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Marco Aiello", "email": "marco.aiello@synlab.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "marioverd", "additionDate": "2025-05-29T09:54:35.422273Z", "lastUpdate": "2025-12-12T10:29:48.030239Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DICOM tags extractor", "description": "Scans the DICOM files of a defined directory at the series level, and produces as output either 1/one single csv file containing all preselected DICOM tags for each detected series; 2/ one single csv file only containing the patientID and the corresponding StudyUIDs.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_tag_selection/info-tab", "biotoolsID": "dicom_tags_extractor", "biotoolsCURIE": "biotools:dicom_tags_extractor", "version": [ "1.1" ], "otherID": [], "relation": [ { "biotoolsID": "eetl_toolset", "type": "usedBy" }, { "biotoolsID": "eucaim_wizard_tool", "type": "usedBy" } ], "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": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "EUCAIM" ], "maturity": "Legacy", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_tag_selection/info-tab", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories", "type": "Software package", "note": "1- Install ORAS tool (https://oras.land/docs/installation).\n2- Login in the registry using the command oras login harbor.eucaim.cancerimage.eu, and provide a username and a token\n3- Download the file by using the command oras pull harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_tag_extraction:1.0", "version": "1.1" } ], "documentation": [ { "url": "https://docs.google.com/document/d/1QCRHohdMe7lX1xTYaw8WxOW_9v2D9EAl/edit", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "BC|Platforms", "email": null, "url": "https://www.bcplatforms.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "lsaint-aubert", "additionDate": "2025-04-18T15:04:18.411979Z", "lastUpdate": "2025-12-12T08:46:59.476389Z", "editPermission": { "type": "group", "authors": [ "ThomasTrouillard" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "metagWGS", "description": "metagWGS is a workflow dedicated to the analysis of metagenomic data. 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Recommends from 8 pipelines: STAR-RSEM-DESeq2 (high accuracy), HISAT2-StringTie-Ballgown (novel transcripts), Salmon-edgeR (balanced), Kallisto-Sleuth (ultra-fast), STAR-HTSeq-limma (complex designs), STAR-featureCounts-NOISeq (non-parametric), Bowtie2-RSEM-EBSeq (Bayesian), HISAT2-Cufflinks-Cuffdiff (legacy). 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