Resource List
List all resources, or create a new resource.
GET /api/t/?documentation=Manual&format=api
{ "count": 4608, "next": "?page=2", "previous": null, "list": [ { "name": "SLiM", "description": "Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.", "homepage": "https://messerlab.org/slim/", "biotoolsID": "SLiM_software", "biotoolsCURIE": "biotools:SLiM_software", "version": [ "4.2.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0550", "term": "DNA substitution modelling" }, { "uri": "http://edamontology.org/operation_0230", "term": "Sequence generation" }, { "uri": "http://edamontology.org/operation_3946", "term": "Ecological modelling" } ], "input": [], "output": [], "note": "Run individual-based eco-evolutionary simulations with explicit genetics", "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://messerlab.org/slim/", "type": [ "Software catalogue" ], "note": "SLiM home page in the Messer Lab website" }, { "url": "https://github.com/MesserLab/SLiM", "type": [ "Repository" ], "note": "GitHub repository for SLiM" }, { "url": "https://groups.google.com/g/slim-discuss", "type": [ "Discussion forum" ], "note": "Discussion forum for SLiM questions" }, { "url": "https://groups.google.com/g/slim-announce", "type": [ "Mailing list" ], "note": "Announcements mailing list" } ], "download": [ { "url": "http://benhaller.com/slim/SLiM.zip", "type": "Source code", "note": "A source archive for the command-line `slim` tool only. Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.", "version": null }, { "url": "https://github.com/MesserLab/SLiM/releases/latest", "type": "Downloads page", "note": "The GitHub page for the current release version, to obtain full source code.", "version": null } ], "documentation": [ { "url": "http://benhaller.com/slim/SLiM_Manual.pdf", "type": [ "User manual" ], "note": "The manual for SLiM itself" }, { "url": "http://benhaller.com/slim/Eidos_Manual.pdf", "type": [ "User manual" ], "note": "The manual for Eidos, the scripting language used by SLiM" }, { "url": "http://benhaller.com/slim/SLiMEidosRefSheets.zip", "type": [ "Quick start guide" ], "note": "Quick reference sheets for SLiM and Eidos" } ], "publication": [ { "doi": "10.1093/molbev/msy228", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": "B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.", "metadata": null }, { "doi": "10.1093/molbev/msy237", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": "B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.", "metadata": null }, { "doi": "10.1111/1755-0998.12968", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": "B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.", "metadata": null }, { "doi": "10.1086/723601", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist 201(5), E127–E139.", "metadata": null } ], "credit": [ { "name": "Philipp Messer", "email": "messer@cornell.edu", "url": "https://messerlab.org", "orcidid": "https://orcid.org/0000-0001-8453-9377", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Benjamin C. Haller", "email": "bhaller@benhaller.com", "url": "http://benhaller.com", "orcidid": "https://orcid.org/0000-0003-1874-8327", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "bchaller", "additionDate": "2019-05-27T16:59:15Z", "lastUpdate": "2024-05-05T19:54:01.119992Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ODAMNet", "description": "A Python package to study molecular relationship between environmental factors and rare diseases.", "homepage": "https://pypi.org/project/ODAMNet/", "biotoolsID": "odamnet", "biotoolsCURIE": "biotools:odamnet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Rare Diseases" ], "link": [ { "url": "https://github.com/MOohTus/ODAMNet", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://odamnet.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2024.101701", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ODAMNet: A Python package to identify molecular relationships between chemicals and rare diseases using overlap, active module and random walk approaches", "abstract": "Environmental factors are external conditions that can affect the health of living organisms. For a number of rare genetic diseases, an interplay between genetic and environmental factors is known or suspected. However, the studies are limited by the scarcity of patients and the difficulties in gathering reliable exposure information. In order to aid in fostering research between environmental factors and rare diseases, we propose ODAMNet, a Python package to investigate the possible relationships between chemicals, which are a subset of environmental factors, and rare diseases. ODAMNet offers three different and complementary bioinformatics approaches for the exploration of relationships: overlap analysis, active module identification and random walk with restart. ODAMNet allows systematic analysis of chemical - rare disease relationships and generation of hypotheses for further investigation of effect mechanisms.", "date": "2024-05-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Terezol M." }, { "name": "Baudot A." }, { "name": "Ozisik O." } ], "journal": "SoftwareX" } } ], "credit": [ { "name": "Morgane Térézol", "email": "morgane.terezol@univ-amu.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-4090-2573", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Anaïs Baudot", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0885-7933", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Ozan Ozisik", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5980-8002", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "mterezol", "additionDate": "2023-03-08T09:19:09.284884Z", "lastUpdate": "2024-05-02T11:58:39.872174Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "JeasyTFM", "description": "Open-source software package for the analysis of large 2D TFM data within ImageJ.", "homepage": "http://questpharma.u-strasbg.fr/JEasyTFM.html", "biotoolsID": "jeasytfm", "biotoolsCURIE": "biotools:jeasytfm", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3934", "term": "Cytometry" }, { "uri": "http://edamontology.org/topic_3318", "term": "Physics" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://questpharma.u-strasbg.fr/JEasyTFM_manual.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOADV/VBAD156", "pmid": "37928344", "pmcid": "PMC10625472", "type": [], "version": null, "note": null, "metadata": { "title": "JEasyTFM: an open-source software package for the analysis of large 2D TFM data within ImageJ", "abstract": "Motivation: Cells adhering to the extracellular matrix can sense and respond to a wide variety of chemical and physical features of the adhesive surface. Traction force microscopy (TFM) allows determining the tensile forces exerted by the cells on their substrate with high resolution. Results: To allow broad access of this techniques to cell biology laboratories we developed JeasyTFM, an open-source ImageJ package able to process multi-color and multi-position time-lapse pictures thus suitable for the automatic analysis of large TFM data.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Carl P." }, { "name": "Ronde P." } ], "journal": "Bioinformatics Advances" } } ], "credit": [ { "name": "Philippe Carl", "email": "philippe.carl@unistra.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-8063-3294", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Philippe Rondé", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-30T12:35:46.193814Z", "lastUpdate": "2024-04-30T12:35:46.196223Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Hybkit", "description": "Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods.", "homepage": "https://pypi.org/project/hybkit/", "biotoolsID": "hybkit", "biotoolsCURIE": "biotools:hybkit", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0463", "term": "miRNA target prediction" }, { "uri": "http://edamontology.org/operation_3792", "term": "miRNA expression analysis" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3794", "term": "RNA immunoprecipitation" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://github.com/RenneLab/hybkit", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://hybkit.readthedocs.io", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAD721", "pmid": "38006335", "pmcid": "PMC10701094", "type": [], "version": null, "note": null, "metadata": { "title": "Hybkit: A Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods", "abstract": "Summary: Experimental methods using microRNA/target ligation have recently provided significant insights into microRNA functioning through generation of chimeric (hybrid) RNA sequences. Here, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence data in the \"hyb\"file format to enable customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes a suite of python objects for developing custom analyses of hybrid data as well as miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA/target interactions in Vienna format.", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Stribling D." }, { "name": "Gay L.A." }, { "name": "Renne R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Daniel Stribling", "email": "ds@ufl.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-0649-9506", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Rolf Renne", "email": "rrenne@ufl.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-7391-8806", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-26T12:47:18.401889Z", "lastUpdate": "2024-04-26T12:47:18.404450Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MCPtaggR", "description": "R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison.", "homepage": "https://github.com/tomoyukif/MCPtaggR", "biotoolsID": "mcptaggr", "biotoolsCURIE": "biotools:mcptaggr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3933", "term": "Demultiplexing" }, { "uri": "http://edamontology.org/operation_0484", "term": "SNP detection" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://tomoyukif.github.io/MCPtaggR/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/DNARES/DSAD027", "pmid": "38134958", "pmcid": "PMC10799318", "type": [], "version": null, "note": null, "metadata": { "title": "MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison", "abstract": "Reduced representation sequencing (RRS) offers cost-effective, high-throughput genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are typically mapped onto a reference genome. However, mapping reads harbouring mismatches against the reference can potentially result in mismapping and biased mapping, leading to the detection of error-prone markers that provide incorrect genotype information. We established a genotype-calling pipeline named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate genotyping by eliminating error-prone markers. MCPtagg was designed for the RRS-based genotyping of a population derived from a biparental cross. The MCPtagg pipeline filters out error-prone markers prior to genotype calling based on marker collinearity information obtained by comparing the genome sequences of the parents of a population to be genotyped. A performance evaluation on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore, our performance test using a genome assembly that was obtained by genome sequence polishing on an available genome assembly suggests that our pipeline performs well with converted genomes, rather than necessitating de novo assembly. This demonstrates its flexibility and scalability. The R package, MCPtaggR, was developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR.", "date": "2024-02-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Furuta T." }, { "name": "Yamamoto T." } ], "journal": "DNA Research" } } ], "credit": [ { "name": "Tomoyuki Furuta", "email": "f.tomoyuki@okayama-u.ac.jp", "url": null, "orcidid": "https://orcid.org/0000-0002-0869-6626", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T10:26:21.921850Z", "lastUpdate": "2024-04-19T10:26:21.924007Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PredictONCO", "description": "A web tool supporting decision-making in precision oncology by extending bioinformatics predictions with advanced computing and machine learning.", "homepage": "https://loschmidt.chemi.muni.cz/predictonco", "biotoolsID": "predictonco", "biotoolsCURIE": "biotools:predictonco", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3938", "term": "Virtual screening" }, { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3577", "term": "Personalised medicine" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://loschmidt.chemi.muni.cz/predictonco/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIB/BBAD441", "pmid": "38066711", "pmcid": "PMC10709543", "type": [], "version": null, "note": null, "metadata": { "title": "PredictONCO: A web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning", "abstract": "PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins frequently altered in various cancer types. The server can assess the impact of mutations on the protein sequential and structural properties and apply a virtual screening to identify potential inhibitors that could be used as a highly individualized therapeutic approach, possibly based on the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art computational tools combined with information from established databases. The user interface was carefully designed for the target specialists in precision oncology, molecular pathology, clinical genetics and clinical sciences. The tool summarizes the effect of the mutation on protein stability and function and currently covers 44 common oncological targets. The binding affinities of Food and Drug Administration/ European Medicines Agency -approved drugs with the wild-type and mutant proteins are calculated to facilitate treatment decisions. The reliability of predictions was confirmed against 108 clinically validated mutations. The server provides a fast and compact output, ideal for the often time-sensitive decision-making process in oncology. Three use cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor in a patient with congenital mismatch repair deficiency highlight how the tool can increase levels of confidence regarding the pathogenicity of the variants and identify the most effective inhibitors. The server is available at https://loschmidt.chemi.muni.cz/predictonco.", "date": "2024-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Stourac J." }, { "name": "Borko S." }, { "name": "Khan R.T." }, { "name": "Pokorna P." }, { "name": "Dobias A." }, { "name": "Planas-Iglesias J." }, { "name": "Mazurenko S." }, { "name": "Pinto G." }, { "name": "Szotkowska V." }, { "name": "Sterba J." }, { "name": "Slaby O." }, { "name": "Damborsky J." }, { "name": "Bednar D." } ], "journal": "Briefings in Bioinformatics" } } ], "credit": [ { "name": "Jiri Damborsky", "email": "jiri@chemi.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "David Bednar", "email": "davidbednar1208@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-6803-0340", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T10:01:19.463835Z", "lastUpdate": "2024-04-19T10:01:19.465909Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Scipion-chem", "description": "An open platform for virtual drug screening.", "homepage": "https://github.com/scipion-chem", "biotoolsID": "scipion_chem", "biotoolsCURIE": "biotools:scipion_chem", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3938", "term": "Virtual screening" }, { "uri": "http://edamontology.org/operation_3899", "term": "Protein-protein docking" }, { "uri": "http://edamontology.org/operation_0416", "term": "Epitope mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_0202", "term": "Pharmacology" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "AGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://scipion-chem.github.io/docs/publications/scipion-chem_vds", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1021/ACS.JCIM.3C01085", "pmid": "38052452", "pmcid": "PMC10751785", "type": [], "version": null, "note": null, "metadata": { "title": "Scipion-Chem: An Open Platform for Virtual Drug Screening", "abstract": "Virtual drug screening (VDS) tackles the problem of drug discovery by computationally reducing the number of potential pharmacological molecules that need to be tested experimentally to find a new drug. To do so, several approaches have been developed through the years, typically focusing on either the physicochemical characteristics of the receptor structure (structure-based virtual screening) or those of the potential ligands (ligand-based virtual screening). Scipion is a workflow engine well suited for structural studies of biological macromolecules. Here, we present Scipion-chem, a new branch oriented to VDS. A total of 11 plugins have already been integrated from the most common programs used in the field. They can be used through the Scipion graphical user interface to execute and analyze typical VDS tasks. In addition, we have developed several consensus protocols that combine results from the different integrated programs to generate more robust predictions. Backstage, Scipion also facilitates the interoperability of those different software packages while tracking all of the intermediate files, parameters, and user decisions. In summary, in this article, we present Scipion-chem. This accessible, interoperable, and traceable platform provides the user with all of the tools to carry out a successful VDS workflow. Scipion-chem is openly available at https://github.com/scipion-chem.", "date": "2023-12-25T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Del Hoyo D." }, { "name": "Salinas M." }, { "name": "Lomas A." }, { "name": "Ulzurrun E." }, { "name": "Campillo N.E." }, { "name": "Sorzano C.O." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "Daniel Del Hoyo", "email": "ddelhoyo@cnb.csic.es", "url": null, "orcidid": "https://orcid.org/0009-0005-3321-1810", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T08:02:22.142231Z", "lastUpdate": "2024-04-19T08:02:22.144325Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TCGAplot", "description": "An R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data.", "homepage": "https://github.com/tjhwangxiong/TCGAplot", "biotoolsID": "tcgaplot", "biotoolsCURIE": "biotools:tcgaplot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_3463", "term": "Expression correlation analysis" }, { "uri": "http://edamontology.org/operation_0490", "term": "Dot plot plotting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/tjhwangxiong/TCGAplot/releases/download/v4.0.0/TCGAplot_4.0.0.zip", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/tjhwangxiong/TCGAplot/blob/main/vignettes/TCGAplot.Rmd", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/tjhwangxiong/TCGAplot/blob/main/vignettes/TCGAplot", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/S12859-023-05615-3", "pmid": "38105215", "pmcid": "PMC10726608", "type": [], "version": null, "note": null, "metadata": { "title": "TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data", "abstract": "Background: Pan-cancer analysis examines both the commonalities and heterogeneity among genomic and cellular alterations across numerous types of tumors. Pan-cancer analysis of gene expression, tumor mutational burden (TMB), microsatellite instability (MSI), and tumor immune microenvironment (TIME), and methylation becomes available based on the multi-omics data from The Cancer Genome Atlas Program (TCGA). Some online tools provide analysis of gene and protein expression, mutation, methylation, and survival for TCGA data. However, these online tools were either Uni-functional or were not able to perform analysis of user-defined functions. Therefore, we created the TCGAplot R package to facilitate perform pan-cancer analysis and visualization of the built-in multi-omic TCGA data. Results: TCGAplot provides several functions to perform pan-cancer paired/unpaired differential gene expression analysis, pan-cancer correlation analysis between gene expression and TMB, MSI, TIME, and promoter methylation. Functions for visualization include paired/unpaired boxplot, survival plot, ROC curve, heatmap, scatter, radar chart, and forest plot. Moreover, gene set based pan-cancer and tumor specific analyses were also available. Finally, all these built-in multi-omic data could be extracted for implementation for user-defined functions, making the pan-cancer analysis much more convenient.\\ Conclusions: We developed an R-package for integrative pan-cancer analysis and visualization of TCGA multi-omics data. The source code and pre-built package are available at GitHub (https://github.com/tjhwangxiong/TCGAplot).", "date": "2023-12-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Liao C." }, { "name": "Wang X." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Xiong Wang", "email": "wangxiong@tjh.tjmu.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T07:46:31.537317Z", "lastUpdate": "2024-04-19T07:46:50.933786Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "hictk", "description": "Blazing fast toolkit to work with .hic and .cool files", "homepage": "https://github.com/paulsengroup/hictk", "biotoolsID": "hictk", "biotoolsCURIE": "biotools:hictk", "version": [ "0.0.1", "0.0.2", "0.0.3", "0.0.4", "0.0.5", "0.0.6", "0.0.7", "0.0.8", "0.0.9", "0.0.10", "0.0.11", "0.0.12" ], "otherID": [], "relation": [ { "biotoolsID": "hictkpy", "type": "usedBy" }, { "biotoolsID": "hictkr", "type": "usedBy" } ], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/paulsengroup/hictk", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/paulsengroup/hictk/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/paulsengroup/hictk/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/hictk", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/paulsengroup/hictk/pkgs/container/hictk", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://hictk.readthedocs.io/en/latest/index.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2023.11.26.568707", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [], "community": null, "owner": "robomics", "additionDate": "2024-02-02T14:42:46.030561Z", "lastUpdate": "2024-04-18T08:55:19.020424Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "oggmap", "description": "Python package to extract gene ages per orthogroup and link them with single-cell RNA data.", "homepage": "https://github.com/kullrich/oggmap", "biotoolsID": "oggmap", "biotoolsCURIE": "biotools:oggmap", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3935", "term": "Dimensionality reduction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://oggmap.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAD657", "pmid": "37952198", "pmcid": "PMC10663984", "type": [], "version": null, "note": null, "metadata": { "title": "oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data", "abstract": "Summary: For model species, single-cell RNA-based cell atlases are available. A good cell atlas includes all major stages in a species’ ontogeny, and soon, they will be standard even for nonmodel species. Here, we propose a Python package called oggmap, which allows for the easy extraction of an orthomap (gene ages per orthogroup) for any given query species from OrthoFinder and other gene family data resources, like homologous groups from eggNOG or PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic species which can be further used to calculate gene age-weighted expression data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited to one transcriptome evolutionary index, oggmap can visualize the individual gene category (e.g. age class, nucleotide diversity bin) and their corresponding expression profiles to investigate scRNA-based cell type assignments in an evolutionary context.", "date": "2023-11-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Ullrich K.K." }, { "name": "Glytnasi N.E." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Kristian K Ullrich", "email": "ullrich@evolbio.mpg.de", "url": null, "orcidid": "https://orcid.org/0000-0003-4308-9626", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Nikoleta E Glytnasi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T14:10:00.623929Z", "lastUpdate": "2024-04-16T14:10:00.646441Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }