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HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Matias Fernandez-Paton", "email": "matias_fernandez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-9374-1411", "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", "Documentor", "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": [ "Documentor", "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": "2025-05-29T09:19:51.404419Z", "lastUpdate": "2026-02-03T11:45:32.223088Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "decompTumor2Sig", "description": "R package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.", "homepage": "http://rmpiro.net/decompTumor2Sig/", "biotoolsID": "decompTumor2Sig", "biotoolsCURIE": "biotools:decompTumor2Sig", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/rmpiro/decompTumor2Sig", "type": [ "Repository" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://rmpiro.net/index.html#downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-019-2688-6", "pmid": "30999866", "pmcid": "PMC6472187", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DecompTumor2Sig: Identification of mutational signatures active in individual tumors", "abstract": "© 2019 The Author(s).Background: The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic processes like age-related spontaneous deamination of 5-methylcytosine. The effect of such mutational processes can be modeled by mutational signatures, of which two different conceptualizations exist: the model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial identification and definition of mutational signatures requires large sets of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use R package that can decompose an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor. Until now, such tools were available only for Alexandrov signatures. We demonstrate the correctness and usefulness of our approach with three test cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor genomes of ten different tumor entities, and from simulated tumor genomes, respectively. Conclusions: The decompTumor2Sig package is freely available and has been accepted for inclusion in Bioconductor.", "date": "2019-04-18T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Kruger S." }, { "name": "Piro R.M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Prof. Dr. Rosario M. Piro", "email": "r.piro@fu-berlin.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "Ruta", "additionDate": "2019-06-20T14:18:28Z", "lastUpdate": "2026-02-02T08:12:42.981321Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-POLIMI" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DrugComb", "description": "The data portal for drug combination and monotherapy sensitivity screenings.\n[v1.5] DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. https://doi.org/10.1093/nar/gkab438\n[v1.4] DrugComb: an integrative cancer drug combination data portal. https://doi.org/10.1093/nar/gkz337", "homepage": "https://researchportal.helsinki.fi/en/datasets/drugcomb/", "biotoolsID": "DrugComb", "biotoolsCURIE": "biotools:DrugComb", "version": [ "1.5" ], "otherID": [], "relation": [ { "biotoolsID": "synergyfinder", "type": "uses" } ], "function": [], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0605", "term": "Informatics" }, { "uri": "http://edamontology.org/topic_3375", "term": "Drug metabolism" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [], "license": "Unlicense", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://researchportal.helsinki.fi/en/datasets/drugcomb/", "type": [ "Repository" ], "note": "alternative links" }, { "url": "https://twitter.com/DrugComb", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://zenodo.org/records/11102665", "type": "Downloads page", "note": "https://zenodo.org/records/11102665", "version": "1.4 summary" }, { "url": "https://zenodo.org/records/15235991", "type": "Downloads page", "note": "https://zenodo.org/records/15235991", "version": "1.5 summary" }, { "url": "https://doi.org/10.5281/zenodo.18449193", "type": "Downloads page", "note": "https://zenodo.org/records/18449193", "version": "1.4 raw" } ], "documentation": [ { "url": "https://researchportal.helsinki.fi/en/datasets/drugcomb/", "type": [ "General" ], "note": null }, { "url": "https://researchportal.helsinki.fi/en/datasets/drugcomb/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/NAR/GKZ337", "pmid": "31066443", "pmcid": "PMC6602441", "type": [ "Primary" ], "version": "1.4", "note": null, "metadata": null }, { "doi": "10.1093/nar/gkab438", "pmid": "34060634", "pmcid": "PMC8218202", "type": [], "version": "1.5", "note": null, "metadata": null } ], "credit": [ { "name": "Jing Tang", "email": "jing.tang@helsinki.fi", "url": null, "orcidid": "https://orcid.org/0000-0001-7480-7710", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jtang920", "additionDate": "2019-08-09T13:06:36Z", "lastUpdate": "2026-02-01T17:44:46.966665Z", "editPermission": { "type": "group", "authors": [ "jtang920" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ELIXIR-CINECA-HPC", "description": "HPC@CINECA provides high-performance computing resources for Elixir members to support large-scale processing and analysis of High-Throughput Sequencing (HTS) data. The service operates on a continuous open-call basis, with approved projects receiving a 1-year allocation that includes 50,000 CPU hours and 1 TB of storage by default, with the possibility to request additional resources. Proposals are evaluated by a scientific committee, with feedback typically provided within seven working days.\n\nFrom 2025, a pilot program enables the analysis of GDPR-protected sensitive data for up to two projects per year (maximum one per user or institution, first-come first-served). Projects involving non-sensitive data are unlimited and may be submitted at any time.", "homepage": "https://docs.google.com/forms/d/e/1FAIpQLSchmLCugIShXAneQmTgbM5SlPLDdZH0KCIECk0R9Tm6GTDcNw/viewform", "biotoolsID": "cineca-hpc", "biotoolsCURIE": "biotools:cineca-hpc", "version": [ "5" ], "otherID": [], "relation": [ { "biotoolsID": "kraken2", "type": "uses" }, { "biotoolsID": "annovar", "type": "uses" }, { "biotoolsID": "tophat2", "type": "uses" }, { "biotoolsID": "bowtie", "type": "uses" }, { "biotoolsID": "bowtie2", "type": "uses" }, { "biotoolsID": "hisat2", "type": "uses" }, { "biotoolsID": "vep", "type": "uses" }, { "biotoolsID": "gatk", "type": "uses" }, { "biotoolsID": "snakemake", "type": "uses" }, { "biotoolsID": "samtools", "type": "uses" }, { "biotoolsID": "R", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "hpc-reditools", "type": "uses" }, { "biotoolsID": "reditools", "type": "uses" }, { "biotoolsID": "tabix", "type": "uses" }, { "biotoolsID": "cutadapt", "type": "uses" }, { "biotoolsID": "fastqc", "type": "uses" }, { "biotoolsID": "multiqc", "type": "uses" }, { "biotoolsID": "trimmomatic", "type": "uses" }, { "biotoolsID": "htseqcount", "type": "uses" }, { "biotoolsID": "deseq2", "type": "uses" }, { "biotoolsID": "plink", "type": "uses" }, { "biotoolsID": "majiq-spel", "type": "uses" }, { "biotoolsID": "stringtie", "type": "uses" }, { "biotoolsID": "bcftools", "type": "uses" }, { "biotoolsID": "limma", "type": "uses" }, { "biotoolsID": "bedtools", "type": "uses" }, { "biotoolsID": "alphafold2", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "bwa-mem2", "type": "uses" }, { "biotoolsID": "cufflinks", "type": "uses" }, { "biotoolsID": "wgsim", "type": "uses" }, { "biotoolsID": "jellyfish", "type": "uses" }, { "biotoolsID": "freebayes", "type": "uses" }, { "biotoolsID": "seqtk", "type": "uses" }, { "biotoolsID": "sra", "type": "uses" }, { "biotoolsID": "varscan", "type": "uses" }, { "biotoolsID": "star", "type": "uses" }, { "biotoolsID": "vcftools", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3760", "term": "Service management" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Bash" ], "license": "Not licensed", "collectionID": [], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://docs.google.com/forms/d/e/1FAIpQLSchmLCugIShXAneQmTgbM5SlPLDdZH0KCIECk0R9Tm6GTDcNw/viewform", "type": [ "Service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://link.springer.com/article/10.1186/s12859-020-03565-8", "type": [ "Other" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-020-03565-8", "pmid": "32838759", "pmcid": "PMC7446135", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1186/s40537-024-01047-9", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Silvia Gioiosa", "email": "s.gioiosa@cineca.it", "url": "https://www.hpc.cineca.it/our-activities/domains/hpc-for-bioinformatics/", "orcidid": "https://orcid.org/0000-0003-1302-8320", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "silvia9", "additionDate": "2026-01-30T11:47:35.909206Z", "lastUpdate": "2026-01-30T12:10:29.923314Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "unexakorea dataset", "description": "This Investigationevaluated the in vivo maintenance effect of a sustained-release vitamin formulation developed using the proprietary coating technology of unexakorea Inc. In a mouse model, the formulation demonstrated a stable plasma concentration for approximately 10–12 hours after administration.\nThese findings suggest that the sustained-release formulation may serve as a promising alternative\nto conventional high-absorption formulations, offering improved physiological stability and reduced\nadverse effects associated with excessive absorption\n\nsustained-release, plasma concentration, Lipid Encapsulation Material", "homepage": "https://unexakorea.com", "biotoolsID": "unexakorea_dataset", "biotoolsCURIE": "biotools:unexakorea_dataset", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3398", "term": "Bioengineering" }, { "uri": "http://edamontology.org/topic_3369", "term": "Chemical biology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], 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With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automatic solution for aligning protein-coding gene datasets containing both functional and nonfunctional sequences (pseudogenes). Through its unique features, reliable codon alignments can be built in the presence of frameshifts and stop codons suitable for subsequent analysis of selection based on the ratio of nonsynonymous to synonymous substitutions. Here we offer a practical overview and guidelines on the use of MACSE v2. This major update of the initial algorithm now comes with a graphical interface providing user-friendly access to different subprograms to handle multiple alignments of protein-coding sequences. We also present new pipelines based on MACSE v2 subprograms to handle large datasets and distributed as Singularity containers. 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