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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Sep 14, 2019)

Physical Resource or Software Tool Software

18 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
RepeatFillerResource, alignment software, image analysis software, data processing software, software resource, software applicationSoftware tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences.Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetectedSCR_017414(RepeatFiller, RRID:SCR_017414)Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany DOI:10.1101/696922Last checked up
PredomicsResource, software resource, software application, source codeSoftware package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data.Metagenomic, data, discover, predictive, signature, unprecedented, interpretability, supervised, learning, ternary, coefficientSCR_017415(Predomics, RRID:SCR_017415)Assistance Publique-Hôpitaux de Paris, EU-FP7, French National AgencyDOI:10.1101/409144Last checked up
Corneal Diseases ClassificationResource, software resource, software application, data processing software, image analysis softwareSoftware based on deep learning model for auto detect corneal diseases. Sample may contain multiple categories. After learning thousands of corneal images, you can make automatic judgments on subtypes of cornea.Deep, learning, model, auto detect, corneal, disease, classificationSCR_017416(Corneal Diseases Classification, RRID:SCR_017416)submitted by: Resource Identification PortalLast checked up
IKAPResource, software resource, software application, data analysis software, data processing softwareSoftware tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation.Identify, cell, population, group, single, cell, RNAseq, analysis, clustering, datasetSCR_017417(IKAP, RRID:SCR_017417)DOI:10.1101/596817Last checked up
SICAS Medical Image RepositoryResource, service resource, data repository, storage service resourceMedical image repository to store medical research data.Medical, image, repository, store, dataSCR_017420(SICAS Medical Image Repository, RRID:SCR_017420)Last checked up
Image Data ResourceResource, service resource, data repository, storage service resourcePublic repository of reference image datasets from published scientific studies. IDR enables access, search and analysis of these highly annotated datasets.Repository, reference, image, published, annotated, datasetSCR_017421(Image Data Resource, RRID:SCR_017421)Last checked up
STRENDA Resource, data or information resource, databaseStorage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal.Storage, Beilstein Institut, functional, enzymology, data, complition, validation, dataset, guideline, standard, reportingSCR_017422(STRENDA , RRID:SCR_017422)Last checked up
European Variation ArchiveResource, service resource, data or information resource, data repository, storage service resource, databaseOpen access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser.Collection, genetic, variation, data, chromosomal, location, dbSNPSCR_017425(European Variation Archive, RRID:SCR_017425)Last checked up
NeurodockerResource, software resource, software applicationSoftware tool to generate Dockerfiles and Singularity recipes for neuroimaging with simple command-line interface. Command line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Supports AFNI, ANTs, Convert3D, Dcm2niix, FreeSurfer, FSL, Matlab Compiler Runtime, MINC, Miniconda, MRtrix3, NeuroDebian, PETPVC, and SPM12.Generate, Dockerfile, singularity, recipe, neuroimaging, command-line, interface, minify, containerSCR_017426(Neurodocker, RRID:SCR_017426)listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked uphttps://www.nitrc.org/projects/neurodocker/
HeuDiConv: a heuristic-centric DICOM converterResource, software resource, software application, data processing softwareSoftware tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts.Flexible, DICOM, converter, organizing, brain, image, data, structured, directory, layoutSCR_017427(HeuDiConv: a heuristic-centric DICOM converter, RRID:SCR_017427)listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked up
Protein Circular Dichroism Data BankResource, service resource, data or information resource, data repository, storage service resource, databasePublic repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. For authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. Includes links for each entry to bioinformatics databases. Data are freely available to accessors either as single files or as complete data bank downloads.SCR_017428(Protein Circular Dichroism Data Bank, RRID:SCR_017428)Birkbeck University of London; London; United Kingdom , Queen Mary University of London; London; United Kingdom International Union of Pure and Applied Chemistry, U.K. Biotechnology and Biological Research CouncilDOI:10.1093/nar/gkw796Last checked up
Inorganic Crystal Structure DatabaseResource, data or information resource, databaseDatabase for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research.Inorganic, crystal, structure, data, atomic, coordinate, quality, FIZ Karlsruhe — Leibniz Institute for Information InfrastructureSCR_017429(Inorganic Crystal Structure Database, RRID:SCR_017429)Last checked up
StatView Version 5.0Resource, software resource, software application, data analysis software, data processing softwareSoftware package for statistical analysis by SAS Institute Inc, Cary, NC.Statistical, analysis, SAS Institute IncSCR_017411(StatView Version 5.0, RRID:SCR_017411)submitted by: Resource Identification PortalLast checked up
dMRIPrepResource, data analysis software, data processing software, software application, 3d spatial image, diffusion-weighted mri 3d image, software resource, mri 3d image, image processing software, image, data or information resourceSoftware tool as preprocessing pipeline for diffusion MRI. Pipeline used for preprocessing of diverse dMRI data. Workflow dispenses of manual intervention, thereby ensuring reproducibility of results.Preprocessing, diffusion, MRI, imaging, dataSCR_017412(dMRIPrep, RRID:SCR_017412)submitted by: Resource Identification PortalLast checked uphttps://doi.org/10.5281/zenodo.3392201
Plant Phenotyping Annotation ToolboxResource, software resource, software toolkitSoftware tool as graphical user interface designed to assist with manual annotation of different parts of the inflorescence. Used in deep plant phenotyping. Works with DeepPod.Manual, annotation, inflorescence, plant, phenotype, annotation, DeepPodSCR_017413(Plant Phenotyping Annotation Toolbox, RRID:SCR_017413)Last checked up
KiMoSysResource, data access protocol, web service, service resource, storage service resource, software resource, data repositoryWeb application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community.Quantitative, kinetic, model, biological, system, data, storage, search, exchange, experimentSCR_017423(KiMoSys, RRID:SCR_017423)EU, Portuguese national funding agency for science, research and technology.Last checked up
The Decoding ToolboxResource, software resource, software application, data analysis software, data processing softwareSoftware Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.Multivariate, analysis, structural, MRI, data, functional, imaging, brainSCR_017424(The Decoding Toolbox, RRID:SCR_017424)German Ministry of Education and Research, German Research FoundationPMID:25610393Last checked up
Open Science FrameworkResource, service resource, portal, data or information resourcePlatform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.Support, enable, collaboration, discover, project, data, materialSCR_017419(Open Science Framework, RRID:SCR_017419)Last checked up
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