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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: Oct 12, 2019)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
SocratesResource, software resourceSoftware for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.genomic rearrangementSCR_006411(Socrates, RRID:SCR_006411)Walter and Eliza Hall Institute of Medical Research; Victoria; Australia Tumor, Cancerlisted by: OMICtoolsPMID:24389656Last checked upOMICS_02200
PIDO - Primary Immunodeficiency Disease OntologyResource, ontology, data or information resource, controlled vocabularyThe Primary Immunodeficiency Disease Ontology Project is developing an ontology for the phenotypic description of Primary Immunodeficiency Diseases. The ontology can be used for integrative research in both biomedical and clinical research. Primary Immunodeficiency Diseases (PIDs) are Mendelian diseases, caused by defects or deletions of genes involved in the development, regulation and maintenance of the immune system. They usually affect newborns and toddlers, but can also manifest much later in life. Information about PIDs is often widely scattered across the research literature and a number of databases. PIDO is an attempt to develop both a machine- as well as a human-comprehensible representation of these diseases, starting with a phenotypic descriptions of disease.phenotype, disease, young human, childSCR_005834(PIDO - Primary Immunodeficiency Disease Ontology, RRID:SCR_005834)Google Project Hosting , Hannover Medical School; Lower Saxony; Germany Primary Immunodeficiency DiseaseBBSRC, DFG, European Union FP7, Hannover Medical School; Lower Saxony; Germanyrelated to: PIDFinderPMID:21949270Last checked upnlx_149345
GASVProResource, software resourceAn algorithm combining both paired read and read depth signals into a probabilistic model which can analyze multiple alignments of reads. It has been used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format. It combines read depth information along with discordant paired-read mappings into a single probabilistic model two common signals of structural variation. When multiple alignments of a read are given, GASVPro utilizes a Markov Chain Monte Carlo procedure to sample over the space of possible alignments.structural variation, genome, genomics, alignment, sequencing, variant, variation, detection, dna, paired, end, read, sequenceSCR_005259(GASVPro, RRID:SCR_005259)Brown University; Rhode Island; USA , Google Code Normal, Cancerlisted by: OMICtoolsPMID:22452995Last checked upOMICS_00317
SRI24 Atlas: Normal Adult Brain AnatomyResource, atlas, reference atlas, data or information resourceAn MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8.analyze, model, magnetic resonance, nifti, nrrd, neuroanatomy, adult human, brain, mri, dtiSCR_002551(SRI24 Atlas: Normal Adult Brain Anatomy, RRID:SCR_002551)Stanford Research Institute International NormalNIA, NIAAAlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:20017133Last checked upnlx_155957
SnpEffResource, software resourceA genetic variant annotation and effect prediction software toolbox that annotates and predicts the effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, javaSCR_005191(SnpEff, RRID:SCR_005191)SourceForge , Wayne State University; Michigan; USA Cancerrelated to: Galaxy, GATK, listed by: OMICtools, works_with: SnpSiftPMID:22728672Last checked upOMICS_00186
nFuseResource, software resourceSoftware that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).cancer, genomicsSCR_000066(nFuse, RRID:SCR_000066)Simon Fraser University; British Columbia; Canada Cancerlisted by: OMICtools, Google CodePMID:22745232Last checked upOMICS_01353
ABIDEResource, data set, data or information resourceResting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included.phenotype, resting state functional magnetic resonance imaging, mri, image, fmriSCR_003612(ABIDE, RRID:SCR_003612) NeuroImaging Tools and Resources Collaboratory (NITRC) , 1000 Functional Connectomes Project Autism spectrum disorder, NormalJoseph P. Healy, Leon Levy Foundation, NIMH, Stavros Niarchos Foundationlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked downnlx_157761
KB Bio 101Resource, ontology, data or information resource, controlled vocabularyOntology of the AURA + Inquire project at SRI International, Menlo Park.owlSCR_010268(KB Bio 101, RRID:SCR_010268)listed by: BioPortalLast checked upnlx_157455
icyResource, image analysis software, data processing software, source code, software application, software repository, software development tool, service resource, software development environment, software resource, image processing softwareAn open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download.image analysis, microscopy, javascript, python, plugin, protocol, scriptSCR_010587(icy, RRID:SCR_010587)Pasteur Institute Centre National de la Recherche Scientifique, French National Research AgencyPMID:22743774Last checked upnlx_45928
SVDetectResource, software resourceSoftware application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perlSCR_010812(SVDetect, RRID:SCR_010812) Curie Institute; Paris; France , SourceForge listed by: OMICtoolsPMID:20639544Last checked upOMICS_00324
ZINBAResource, software resourceSoftware to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.SCR_010868(ZINBA, RRID:SCR_010868)University of North Carolina at Chapel Hill; North Carolina; USA listed by: OMICtoolsPMID:21787385Last checked upOMICS_00465
CUDA-ECResource, software resourceA fast parallel error correction tool for short reads.c, gpu/cudaSCR_001090(CUDA-EC, RRID:SCR_001090)SourceForge listed by: OMICtoolsPMID:20426693Last checked upOMICS_01100
BASEResource, software resourceA comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software.SCR_010937(BASE, RRID:SCR_010937)Lund University; Lund; Sweden listed by: OMICtoolsPMID:19822003Last checked upOMICS_00749
massiRResource, software resourceSoftware that predicts the sex of samples in gene expression microarray datasets.standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality controlSCR_001157(massiR, RRID:SCR_001157)Bioconductor listed by: OMICtoolsPMID:24659105Last checked upOMICS_03638
ngs.plotResource, software resourceA software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.SCR_011795(ngs.plot, RRID:SCR_011795)Google Code listed by: OMICtoolsLast checked upOMICS_00922
InfernalResource, software resourceSoftware for searching DNA sequence databases for RNA structure and sequence similarities.SCR_011809(Infernal, RRID:SCR_011809)Janelia Research related to: ANNOgesic, listed by: OMICtoolsPMID:24008419Last checked upOMICS_00977
discovering-cseResource, software resourceSoftware for discovering motifs that induce sequencing errors.motifSCR_011832(discovering-cse, RRID:SCR_011832)Google Code listed by: OMICtoolsLast checked upOMICS_01040
PatMaNResource, software resourceSoftware that searches for short patterns in large DNA databases, allowing for approximate matches.c++SCR_011821(PatMaN, RRID:SCR_011821)listed by: OMICtoolsPMID:18467344Last checked upOMICS_00997
Baa.plResource, software resourceSoftware tool to evaluate de novo genome assemblies with RNA transcripts.genomics, genome assembly, rna transcript, perlSCR_001197(, RRID:SCR_001197)listed by: OMICtoolsLast checked downOMICS_02154
orthAgogueResource, software resourceA software tool for high speed estimation of homology relations within and between species in massive data sets.unix/linuxSCR_011979(orthAgogue, RRID:SCR_011979)Google Code listed by: OMICtoolsPMID:24115168Last checked upOMICS_01691
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