SIGNALSIGNAL (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.https://signal.niaid.nih.govsignalbiotools:signalWeb applicationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_2229Cell biologyRhttp://edamontology.org/operation_3928Pathway analysishttp://edamontology.org/operation_3927Network analysis10.1016/j.cels.2021.03.00133894945PMC7613048PrimaryIain D.C. Fraserfraseri@nih.govPersonPrimary contactSignalPPrediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.http://cbs.dtu.dk/services/SignalP/signalpbiotools:signalp4.1rrid:SCR_015644rridCommand-line toolWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxMacOtherCBSMatureFree of charge (with restrictions)http://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTApredicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organismshttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpRepositoryhttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpSource codehttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpBinarieshttp://www.cbs.dtu.dk/services/SignalPGeneral10.1038/nmeth.170121959131PrimaryTN PetersenPersonDeveloperCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643DeveloperHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643PersonPrimary contactSignacXCell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts.
Get the most out of your single cell data.
SignacX 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.https://github.com/mathewchamberlain/SignacXsignacxbiotools:signacxDesktop applicationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3170RNA-SeqRGPL-3.0http://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3802Sortinghttp://edamontology.org/operation_3435Standardisation and normalisation10.1101/2021.02.01.42920710.21203/RS.3.RS-199733/V1Virginia SavovaVirginia.Savova@sanofi.comPersonSignacMultimodal single-cell chromatin analysis with Signac.
A New Algorithm for Finding Marker Genes in Single-Cell Transcriptomic Data.
Signac - A versatile package for Single-cell RNA-Seq analysis.
We 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.
Signac is an extension of Seurat for the analysis of single-cell chromatin data.https://satijalab.org/signac/signacbiotools:signachttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3512Gene transcriptsC++RPythonhttp://edamontology.org/operation_3222Peak callinghttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3891Essential dynamicshttps://github.com/bioturing/signacRepositoryhttps://cloud.r-project.org/package=SignacOtherhttps://github.com/timoast/signacRepositoryhttps://github.com/timoast/signac-paperRepository10.1101/2020.11.09.37361310.1101/2020.11.16.384479Tim Stuarttstuart@nygenome.orgPersonRahul Satijarsatija@nygenome.orgPersonSon Phamsonpham@bioturing.comPersoneSIGNALeSignal 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.http://motif.stanford.edu/distributions/esignal/esignalbiotools:esignal1.0Command-line toolhttp://edamontology.org/topic_0078ProteinsLinuxC++PerlChttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/esignal-1-0-database-medline-mesh-terms-protein-motifs-detect-signal-transduction-proteins.htmlSoftware cataloguehttp://motif.stanford.edu/distributions/esignal/User manualhttp://motif.stanford.edu/PersonPrimary contact