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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 3, 2019)

Physical Resource or Software Tool Software

201 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
PindelResource, software resourceSoftware to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpointSCR_000560(Pindel, RRID:SCR_000560)Washington University School of Medicine in St. Louis; Missouri; USA listed by: OMICtools, works_with: cgpPindelPMID:19561018Last checked downOMICS_00321
GenoViewerResource, software resourceOpen source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing sequencing, sequence, mutation, windows, linux, mac os x, genome, browser, sam, bam, fasta, gff, read error, snp, mnp, insertion, deletionSCR_001203(GenoViewer, RRID:SCR_001203)listed by: OMICtoolsLast checked downOMICS_02146
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
BSSimResource, software resourceSoftware to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD.bisulfite sequencing, simulator, next-generation sequencing, python, dna methylation, snp, read qualitySCR_001212(BSSim, RRID:SCR_001212)listed by: OMICtoolsLast checked downOMICS_02130
lesResource, software resourceSoftware package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcriptionSCR_001291(les, RRID:SCR_001291)Bioconductor listed by: OMICtoolsLast checked downOMICS_02045
virtualArrayResource, software resourceSoftware package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array.microarray, preprocessingSCR_001361(virtualArray, RRID:SCR_001361) University of Leipzig; Saxony; Germany , Bioconductor listed by: OMICtoolsPMID:23452776Last checked downOMICS_01979
Drosophila anatomy and development ontologiesResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.anatomy, development, developmental stage, gene expression, phenotype, owlSCR_001607(Drosophila anatomy and development ontologies, RRID:SCR_001607) SourceForge , FlyBase NHGRIrelated to: OBO, Flannotator, REDfly- Regulatory Element Database for Drosophilia, Bgee: a dataBase for Gene Expression EvolutionLast checked downnlx_153871
NIF Web ServicesResource, web service, software resource, data access protocolRepresentational State Transfer (REST) model based service for accessing a set of Neuroscience Information Framework (NIF) data through a fixed set of operations. They are defined by a WADL file which allows clients to automatically generate code for these services. The services (AnnotateService, FederationService, LdaService, LexicalService, LiteratureService, QueryService, SummaryService, VocabularyService) include the ability to: * Retrieve a federation summary, e.g.,* * Retrieve data records from a NIF federation source for a search, e.g., * Retrieve registry data records from NIF, e.g., * Retrieve a complete search summary, e.g., * Retrieve NIF auto-complete suggestions, e.g., * Use the NIF annotator for arbitrary text, e.g., These services are documented for developers in the WADL file (and client stubs should have the comments embedded in them). Visit, for more informationrest, data sharing, wadlSCR_001631(NIF Web Services, RRID:SCR_001631)Neuroscience Information Framework related to: SciCrunch Registry, NIF Literature, OntoQuest, used by: NIF Data FederationLast checked downnlx_153899
STAPLEResource, software resource, software applicationAn algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion.algorithm, analyze, c++, dicom, gifti, image display, linux, macos, microsoft, magnetic resonance, nifti, nrrd, posix/unix-like, quantification, rendering, segmentation, surface rendering, visualization, win32 (ms windows), windows, standardSCR_002590(STAPLE, RRID:SCR_002590)Harvard Medical School; Massachusetts; USA listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:15250643Last checked downnlx_155994
Primer DesignerResource, software resourceSoftware program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki.primer, primer designSCR_003189(Primer Designer, RRID:SCR_003189)listed by: OMICtoolsLast checked downOMICS_02327
Ontology Development and Information ExtractionResource, software resource, software toolkit, source codeA software toolkit to code document sets with ontologies or to enrich existing ontologies with new concepts from the document set. It contains algorithms for Named Entity Recognition, Co-reference resolution, concept discovery, discourse reasoning and attribute value extraction. The project aimed to develop a toolkit that will provide the following functionality: * Build text processing pipelines that use ontologies to annotate documents. * Enrich ontologies with new concepts that are automatically discovered in documents. * Populate an information model automatically from information extracted from documents. ODIE is open source software released under the LGPL v3.0 License. ODIE is written in Java and uses the Eclipse RCP Framework for the UI. The source code is organized into Eclipse projects.ontology, annotation, named entity recognition, java, ontology enrichment, information extraction, natural language processingSCR_003405(Ontology Development and Information Extraction, RRID:SCR_003405)Stanford University; Stanford; California listed by: 3DVC, FORCE11, BiositemapsLast checked downnif-0000-33009
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
BabelResource, software resource, software application, data analysis software, data processing softwareSoftware that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA countswindows, macos xSCR_004307(Babel, RRID:SCR_004307)University of California at San Francisco; California; USA listed by: OMICtoolsLast checked downOMICS_01530
ShoRAHResource, software resourceA software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.linux, mac os x, windows, next-generation sequencing, c++, python, perl, structure, population, short sequence read, haplotypeSCR_005211(ShoRAH, RRID:SCR_005211)ETH Zurich; Zurich; Switzerland listed by: OMICtoolsPMID:21521499Last checked downOMICS_00231
ABS filterResource, software resourceR package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.unix/linuxSCR_005328(ABS filter, RRID:SCR_005328)Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland listed by: OMICtoolsPMID:24255646Last checked downOMICS_00427
YabiResource, software resource, service resourceA web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts.grid computing, high performance computing, cloud computing, bioinformatics, pipeline, workflow, command line, python, linux, storage, compute, genomics, transcriptomics, proteomicsSCR_005359(Yabi, RRID:SCR_005359)Murdoch University; Perth; Australia listed by: OMICtoolsPMID:22333270Last checked downOMICS_01148
SAAP-RRBSResource, software resourceStreamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing.genomics, next generation sequencingSCR_006516(SAAP-RRBS, RRID:SCR_006516)Google Code listed by: OMICtoolsLast checked upOMICS_00612
simhtsdResource, software resourceSoftware that given a reference sequence, will create a large set of short nucleotide reads, simulating the output from today''s high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.command-line, perlSCR_006822(simhtsd, RRID:SCR_006822)SourceForge listed by: OMICtoolsLast checked upOMICS_00256
HLASeqResource, software resourceAn open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.genotyping, hla, next generation sequencing, gene, command-line, pythonSCR_004185(HLASeq, RRID:SCR_004185)SourceForge listed by: OMICtoolsLast checked upOMICS_01543
hiCtoolsResource, software resourceThis collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.SCR_013010(hiCtools, RRID:SCR_013010)SourceForge listed by: OMICtoolsLast checked upOMICS_00522
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