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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: Aug 10, 2019)

Physical Resource or Software Tool Software

16,721 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Diffusion ToolkitResource, software resource, software application, data analysis software, data processing softwareSoftware as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.data, reconstruction, fiber, tracking, diffusion, MR, image, processing, tractographySCR_017345(Diffusion Toolkit, RRID:SCR_017345)Harvard University; Cambridge; United States listed by: OMICtools, NITRCLast checked uphttps://cds.ismrm.org/ismrm-2007/files/03720.pdf, https://www.nitrc.org/projects/trackvis/
Cell Ranger Resource, software resource, software application, data analysis software, data processing softwareSoftware tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.Analysis, process, chromium, singe, cell, RNA-seq, align, read, barcode, matrice, clustering, gene, expression, 10xGenomicsSCR_017344(Cell Ranger , RRID:SCR_017344)Last checked up
apeResource, software resource, software application, data analysis software, data processing softwareSoftware R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.analysis, phylogenetics, evolutionSCR_017343(ape, RRID:SCR_017343)related to: CRANPMID:30016406Last checked uphttps://cran.r-project.org/web/packages/ape/ape.pdf, http://ape-package.ird.fr/
Connectome Computation SystemResource, software resource, software application, data analysis software, data processing softwareSoftware tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonanceSCR_017342(Connectome Computation System, RRID:SCR_017342)DOI:10.1007/s11434-014-0698-3Last checked up
ITK-SNAPResource, segmentation software, image analysis software, data processing software, software resource, software applicationSoftware as open source, multiplatform tool used to segment structures in 3D medical images.multiplatform, segment, sturcture, 3D, medical, imageSCR_017341(ITK-SNAP, RRID:SCR_017341) University of Utah; Utah; USA , University of Pennsylvania; Philadelphia; Pennsylvania NIBIBLast checked up
HorosResource, data visualization software, software application, data processing software, software resourceSoftware tool as open source medical image viewer. Enables to browse and visualize medical imaging libraries.Medical, image, viewer, ivisualize, medical, imaging, librarySCR_017340(Horos, RRID:SCR_017340)Last checked up
ScfindResource, software resource, software application, data processing software, data or information resourceSoftware R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed.Single, cell, RNA-seq, data, gene, list, build, index, organizeSCR_017339(Scfind, RRID:SCR_017339)Wellcome Trust Sanger Institute; Hinxton; United Kingdom listed by: BioconductorLast checked uphttps://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind
ScmapResource, software resource, software application, data processing softwareSoftware tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments.Unsupervised, projection, single, cell, RNA-seq, dataSCR_017338(Scmap, RRID:SCR_017338)Wellcome Trust Sanger Institute; Hinxton; United Kingdom listed by: BioconductorPMID:29608555Last checked uphttp://bioconductor.org/packages/scmap/, https://www.sanger.ac.uk/science/tools/scmap
OGDrawResource, data processing software, software application, data visualization software, service resource, software resource, software toolkitSoftware package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers.graphical, visualization, organellar, genome, convert, annotation, GenBank, format, map, DNA, sequenceSCR_017337(OGDraw, RRID:SCR_017337)Max Planck Societyworks_with: GenBankPMID:30949694Last checked up
GeSeq Resource, software resource, software application, service resource, data processing softwareSoftware tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.rapid, accurate, annotation, organelle, genome, chloroplastSCR_017336(GeSeq , RRID:SCR_017336)German Science Foundation, Human Frontier Science Program, Max Planck Societylisted by: OMICtoolsPMID:28486635Last checked up
NOVOPlastyResource, alignment software, image analysis software, data processing software, software resource, software applicationSoftware package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data.de novo, assembler, heteroplasmy, variance, caller, short, circular, genome, organelle, whole, dataSCR_017335(NOVOPlasty, RRID:SCR_017335)Belgian Kids Fund, Hôpital Universitaire des Enfants Reine Fabiola, Interuniversity Institute of Bioinformatics in Brusselslisted by: OMICtoolsPMID:28204566Last checked up
trimAlResource, software resource, software application, data analysis software, data processing softwareSoftware tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysisSCR_017334(trimAl, RRID:SCR_017334)FIS, MEClisted by: OMICtoolsPMID:19505945Last checked uphttps://vicfero.github.io/trimal/
PILERResource, software resource, software application, data analysis software, data processing softwareSoftware tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.analysis, repetitive, DNA, genome, sequence, classification, alignmentSCR_017333(PILER, RRID:SCR_017333)listed by: OMICtoolsPMID:15961452Last checked uphttps://omictools.com/piler-tool
GCEResource, software resource, software application, data analysis software, data processing softwareSoftware tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.estimation, genomic, characteristic, analysis, k-mer, frequencey, de novoSCR_017332(GCE, RRID:SCR_017332)Last checked upftp://ftp.genomics.org.cn/pub/gce
ProovreadResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationSoftware tool for PacBio hybrid error correction through iterative short read consensus.PacBio, hybrid, error, correction, short, read, consensus, DNA, sequencingSCR_017331(Proovread, RRID:SCR_017331)European Research Councilrelated to: BWA, BLASR, SHRiMPPMID:25015988Last checked up
SynGOResource, data analysis service, production service resource, analysis service resource, service resource, ontology, controlled vocabulary, data or information resourceEvidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotationSCR_017330(SynGO, RRID:SCR_017330)CERCA Program/Generalitat de Catalunya, European Union, German Federal Ministry of Education and Research, NINDS, Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvarduses: Gene Ontology, submitted by: Neuroscience Information FrameworkPMID:31171447Last checked up
Sample Size MattersResource, narrative resource, short course material, training material, data or information resourceTen hour course describing sample size calculations, when they can and should be used. Online program for graduate students and research professionals. Participants learn to apply knowledge and skills gained to improve rigor, transparency and reproducibility in their own research.course, program, graduate, student, researcher, sample, size, calculation, Mayo ClinicSCR_017329(Sample Size Matters, RRID:SCR_017329)Mayo Clinic submitted by: Resource Identification PortalLast checked up
OntoSoftResource, software resource, software repository, portal, data or information resourcePlatform to provide community repository for geosciences software. Registry for software for geoscientists. Part of NSF EarthCube OntoSoft project.registry, software, repository, geoscientistSCR_017328(OntoSoft, RRID:SCR_017328)submitted by: Resource Identification PortalLast checked up
fiddleResource, software resource, software application, service resourceSoftware interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community.identify, publication, format, dataset, null, result, file, drawer, data, liberation, effortSCR_017327(fiddle, RRID:SCR_017327)submitted by: Resource Identification PortalDOI:10.31219/osf.io/6mcu3Last checked uphttps://github.com/quest-bih/FIDDLE
University of Johannesburg; Johannesburg; South AfricaOrganizationPublic university located in Johannesburg, South Africa. Came into existence on 1 January 2005 as result of merger between Rand Afrikaans University, Technikon Witwatersrand and Soweto and East Rand campuses of Vista University.SCR_017326(University of Johannesburg; Johannesburg; South Africa, RRID:SCR_017326)Last checked up
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