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"http://edamontology.org/format_2305", "term": "GFF" } ] }, { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] } ], "note": "predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": "Other", "collectionID": [ "CBS" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.cbs.dtu.dk/cgi-bin/sw_request?signalp", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://www.cbs.dtu.dk/cgi-bin/sw_request?signalp", "type": "Source code", "note": null, "version": null }, { "url": "http://www.cbs.dtu.dk/cgi-bin/sw_request?signalp", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://www.cbs.dtu.dk/services/SignalP", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.1701", "pmid": "21959131", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SignalP 4.0: Discriminating signal peptides from transmembrane regions", "abstract": "", "date": "2011-10-01T00:00:00Z", "citationCount": 6571, "authors": [ { "name": "Petersen T.N." }, { "name": "Brunak S." }, { "name": "Von Heijne G." }, { "name": "Nielsen H." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "TN Petersen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "CBS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Henrik Nielsen", "email": "hnielsen@cbs.dtu.dk", "url": null, "orcidid": "http://orcid.org/0000-0002-9412-9643", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Henrik Nielsen", "email": "hnielsen@cbs.dtu.dk", "url": null, "orcidid": "http://orcid.org/0000-0002-9412-9643", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "lidiamorrone", "additionDate": "2015-12-17T14:23:00Z", "lastUpdate": "2023-10-17T12:15:14.583961Z", "editPermission": { "type": "group", "authors": [ "CBS", "lidiamorrone", "Medicine" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SIGNAL", "description": "SIGNAL (Selection by Iterative pathway Group and Network Analysis Looping) is a web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays.", "homepage": "https://signal.niaid.nih.gov", "biotoolsID": "signal", "biotoolsCURIE": "biotools:signal", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3928", "term": "Pathway analysis" }, { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1016/J.CELS.2021.03.001", "pmid": "33894945", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays", "abstract": "Copyright © 2021. Published by Elsevier Inc.Hit selection from high-throughput assays remains a critical bottleneck in realizing the potential of omic-scale studies in biology. Widely used methods such as setting of cutoffs, prioritizing pathway enrichments, or incorporating predicted network interactions offer divergent solutions yet are associated with critical analytical trade-offs. The specific limitations of these individual approaches and the lack of a systematic way by which to integrate their rankings have contributed to limited overlap in the reported results from comparable genome-wide studies and costly inefficiencies in secondary validation efforts. Using comparative analysis of parallel independent studies as a benchmark, we characterize the specific complementary contributions of each approach and demonstrate an optimal framework to integrate these methods. We describe selection by iterative pathway group and network analysis looping (SIGNAL), an integrated, iterative approach that uses both pathway and network methods to optimize gene prioritization. SIGNAL is accessible as a rapid user-friendly web-based application (https://signal.niaid.nih.gov). A record of this paper's transparent peer review is included in the Supplemental information.", "date": "2021-04-21T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Katz S." }, { "name": "Song J." }, { "name": "Webb K.P." }, { "name": "Lounsbury N.W." }, { "name": "Bryant C.E." }, { "name": "Fraser I.D.C." } ], "journal": "Cell systems" } } ], "credit": [ { "name": "Iain D.C. Fraser", "email": "fraseri@nih.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "Kigaard", "additionDate": "2021-12-06T08:04:19.170561Z", "lastUpdate": "2021-12-06T08:04:19.173001Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SignacX", "description": "Cell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts.\n\nGet the most out of your single cell data.\n\nSignacX is software developed and maintained by the Savova lab at Sanofi with a focus on single cell genomics for clinical applications. SignacX classifies the cellular phenotype for each individual cell in single cell RNA-sequencing data using neural networks trained with sorted bulk gene expression data from the Human Primary Cell Atlas. To learn more, check out the pre-print, website and code base.", "homepage": "https://github.com/mathewchamberlain/SignacX", "biotoolsID": "signacx", "biotoolsCURIE": "biotools:signacx", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2021.02.01.429207", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.21203/RS.3.RS-199733/V1", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Virginia Savova", "email": "Virginia.Savova@sanofi.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "zsmag19", "additionDate": "2021-03-19T09:09:08Z", "lastUpdate": "2021-04-09T09:45:26Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Signac", "description": "Multimodal single-cell chromatin analysis with Signac.\n\nA New Algorithm for Finding Marker Genes in Single-Cell Transcriptomic Data.\n\nSignac - A versatile package for Single-cell RNA-Seq analysis.\n\nWe introduce Signac, a versatile R package to facilitate the analysis workflow for single-cell data. It helps to find marker genes faster and more accurate, search for cells with similar expression profiles, integrate multiple datasets in the BioTuring Browser database (know more about BioTuring Browser), etc. For users with a limited computational resource, we provide the helper functions to exercise all analyses for the large-scale datasets from disk. Because of its speed and flexibility, it can be adapted to any existing R analysis pipeline to help explore single-cell data more efficient.\n\nSignac is an extension of Seurat for the analysis of single-cell chromatin data.", "homepage": "https://satijalab.org/signac/", "biotoolsID": "signac", "biotoolsCURIE": "biotools:signac", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3222", "term": "Peak calling" }, { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" }, { "uri": "http://edamontology.org/operation_3935", "term": "Dimensionality reduction" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" } ], "operatingSystem": [], "language": [ "C++", "R", "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioturing/signac", "type": [ "Repository" ], "note": null }, { "url": "https://cloud.r-project.org/package=Signac", "type": [ "Other" ], "note": null }, { "url": "https://github.com/timoast/signac", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/timoast/signac-paper", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2020.11.09.373613", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1101/2020.11.16.384479", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Tim Stuart", "email": "tstuart@nygenome.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Rahul Satija", "email": "rsatija@nygenome.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Son Pham", "email": "sonpham@bioturing.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "zsmag19", "additionDate": "2021-01-18T11:49:42Z", "lastUpdate": "2021-02-18T17:31:47Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "eSIGNAL", "description": "eSignal is a database of eMOTIFs and eMATRICES generated exclusively from signal transduction proteins. ESIGNAL can be used to discover signal transduction functions in new proteins.", "homepage": "http://motif.stanford.edu/distributions/esignal/", "biotoolsID": "esignal", "biotoolsCURIE": "biotools:esignal", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux" ], "language": [ "C++", "Perl", "C" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/esignal-1-0-database-medline-mesh-terms-protein-motifs-detect-signal-transduction-proteins.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://motif.stanford.edu/distributions/esignal/", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": null, "email": null, "url": "http://motif.stanford.edu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "mbs_import", "additionDate": "2017-12-18T00:14:48Z", "lastUpdate": "2018-12-10T12:58:52Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }