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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Rat Strain Ontology
 
Resource Report
Resource Website
1+ mentions
Rat Strain Ontology (RRID:SCR_003449) data or information resource, ontology, controlled vocabulary Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. rat strain, obo, gene, pathway, biological process, metabolic, regulatory, signaling, drug, disease, metabolic pathway, regulatory pathway, signaling pathway, drug pathway, disease pathway, gene is listed by: BioPortal
is listed by: OBO
has parent organization: Rat Genome Database (RGD)
Free, Freely available nlx_157569, nlx_157544, SCR_003473 http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001
http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457
http://purl.bioontology.org/ontology/RS
ftp://rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo
SCR_003449 2026-02-14 02:00:49 1
Phenotree
 
Resource Report
Resource Website
Phenotree (RRID:SCR_003591) Phenotree data or information resource, service resource, data set Web server to search for genes involved in given phenotypic difference between mammalian species. The mouse-referenced multiple alignment data files used to perform the forward genomics screen is also available. The webserver implements one strategy of a Forward Genomics approach aiming at matching phenotype to genotype. Forward genomics matches a given pattern of phenotypic differences between species to genomic differences using a genome-wide screen. In the implementation, the divergence of the coding region of genes in mammals is measured. Given an ancestral phenotypic trait that is lost in independent mammalian lineages, it is shown that searching for genes that are more diverged in all trait-loss species can discover genes that are involved in the given phenotype. gene, genotype, phenotype, alignment, trait, genome, alignment is related to: UCSC Genome Browser
has parent organization: Stanford University; Stanford; California
PMID:23022484 Acknowledgement requested, Non-commercial, Free for personal use, Http://stanford.edu/site/terms.html nlx_157736 SCR_003591 Forward Genomics - Phenotree server, Forward Genomics - Phenotree search 2026-02-14 02:00:50 0
EPIGEN
 
Resource Report
Resource Website
10+ mentions
EPIGEN (RRID:SCR_000093) EPIGEN data or information resource, organization portal, portal, consortium THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. epilepsy, genetics, gene, mri, genetic variation, clinical has parent organization: Duke University; North Carolina; USA
has parent organization: University College London; London; United Kingdom
has parent organization: Beaumont Hospital; Dublin; Ireland
has parent organization: Royal College of Surgeons in Ireland; Dublin; Ireland
has parent organization: Free University of Brussels; Brussels; Belgium
Epilepsy THIS RESOURCE IS NO LONGER IN SERVICE nlx_143740 SCR_000093 EPIGEN: An international consortium dedicated to tackling epilepsy through genetics, EPIGEN Consortium 2026-02-14 01:59:36 24
RSEM
 
Resource Report
Resource Website
50+ mentions
RSEM (RRID:SCR_000262) data analysis software, software resource, data processing software, software application Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools is listed by: OMICtools
is listed by: GitHub
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Wisconsin-Madison; Wisconsin; USA
PMID:21816040 Free, Available for download, Freely available OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 https://github.com/deweylab/RSEM
https://github.com/deweylab/RSEM/releases
https://bio.tools/rsem
https://sources.debian.org/src/rsem/
SCR_000262 RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 2026-02-14 01:59:40 94
iFad
 
Resource Report
Resource Website
iFad (RRID:SCR_000271) iFad software resource An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines. r, gene expression, drug sensitivity, analysis, drug-pathway association, gene-pathway, pathway, gene, drug is listed by: OMICtools
has parent organization: Yale School of Medicine; Connecticut; USA
PMID:22581178 Free, Available for download, Freely available OMICS_01959 SCR_000271 2026-02-14 01:59:40 0
High-Throughput GoMiner
 
Resource Report
Resource Website
1+ mentions
High-Throughput GoMiner (RRID:SCR_000173) software resource, web application THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories. term enrichment, gene ontology, gene, microarray, common variable immune deficiency, high-throughput, visualization, database is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: GoMiner
has parent organization: National Cancer Institute
has parent organization: National Cancer Institute
NCI 1Z01BC010842-01 PMID:15998470 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149300 SCR_000173 2026-02-14 01:59:38 2
GPViz
 
Resource Report
Resource Website
GPViz (RRID:SCR_000346) GPViz software resource A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants. gene, visualization, genomic, variant, bioinformatics, java is listed by: OMICtools Free, Available for download, Freely available OMICS_00915 SCR_000346 2026-02-14 01:59:41 0
TEDDY
 
Resource Report
Resource Website
1+ mentions
TEDDY (RRID:SCR_000383) TEDDY clinical trial, portal, consortium, data or information resource, organization portal, database International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes. consortium, gene, infectious agent, dietary factor, environmental factor, young human, insulin, child, pediatric, autoantibody, blood, stool, biomaterial supply resource, longitudinal, neonate, parent, genetic risk, genetic factor, observation, prospective, serum, plasma, peripheral blood mononuclear cell, saliva, nasal swab, nail clipping, water, dna, virus, nutrition, toxic agent, socioeconomic, psychosocial, male, female, environment, exposure, diet, toxin, infectious agent, bacterial, viral, immunization is listed by: One Mind Biospecimen Bank Listing
is listed by: ClinicalTrials.gov
is listed by: NIDDK Information Network (dkNET)
is listed by: NIDDK Central Repository
is related to: Teddy study IA prediction
has parent organization: University of South Florida; Florida; USA
Type 1 diabetes, Diabetes NIDDK 2UC4DK063829 PMID:21564455 nlx_152857 SCR_000383 The Environmental Determinants of Diabetes in the Young, TEDDY study 2026-02-14 01:59:44 3
ARB project
 
Resource Report
Resource Website
10+ mentions
ARB project (RRID:SCR_000515) ARB software resource Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations. rrna sequence, rrna, phylogeny, alignment, analysis, protein, gene is listed by: Debian
is related to: SILVA
is related to: SINA
has parent organization: Technical University of Munich; Bavaria; Germany
PMID:14985472 Free, Available for download, Freely available OMICS_01515 https://sources.debian.org/src/arb/ SCR_000515 The ARB project 2026-02-14 01:59:45 28
RefFinder
 
Resource Report
Resource Website
10+ mentions
RefFinder (RRID:SCR_000472) RefFinder web service, analysis service resource, production service resource, service resource, data access protocol, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, gene expression, reference gene, web based tool uses: BestKeeper
uses: NormFinder
uses: geNORM
is listed by: OMICtools
has parent organization: East Carolina University; Carolina; USA
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02321 http://www.leonxie.com/referencegene.php SCR_000472 2026-02-14 01:59:44 45
FlyBrain
 
Resource Report
Resource Website
1+ mentions
FlyBrain (RRID:SCR_000706) data processing software, training resource, data or information resource, atlas, software application, software resource, narrative resource, training material THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Interactive database of Drosophila melanogaster nervous system. Used by drosophila neuroscience community and by other researchers studying arthropod brain structure. drosophila melanogaster, ganglion, gene, 3-dimensional, abdominal, anatomy, arthropod, autofluorescence, chemical, development, developmental, golgi, histology, immunocytology, impregnation, map, model, morphology, nervous system, neuroanatomical, neuroanatomy, neuron, neuropil, periphery, phenotype, structure, thoracic, visualization has parent organization: National Institute for Basic Biology; Okazaki; Japan
has parent organization: University of Arizona; Arizona; USA
has parent organization: University of Freiburg; Baden-Wurttemberg; Germany
PMID:8592752
PMID:21280038
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00031 SCR_000706 FlyBrain 2026-02-14 01:59:47 3
PiNGO
 
Resource Report
Resource Website
PiNGO (RRID:SCR_000692) PiNGO software resource A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, annotation, network, candidate gene, biological network, ontology or annotation search engine, statistical analysis, term enrichment, functional similarity, functional prediction, search engine, windows, mac os x, linux, unix is listed by: Gene Ontology Tools
is listed by: OMICtools
is related to: Gene Ontology
is related to: Cytoscape
has parent organization: Ghent University; Ghent; Belgium
PMID:21278188 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149330, OMICS_02281 SCR_000692 2026-02-14 01:59:49 0
Baylor College of Medicine - Shaw Laboratory
 
Resource Report
Resource Website
1+ mentions
Baylor College of Medicine - Shaw Laboratory (RRID:SCR_000604) BCM - Shaw Laboratory, BCM Shaw Laboratory, BCM Shaw Lab laboratory portal, data or information resource, organization portal, portal The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare. statistics, bioinformatics, analysis, genomic, gene, biological process has parent organization: Baylor University; Texas; USA THIS RESOURCE IS NO LONGER IN SERVICE nlx_149156 SCR_000604 2026-02-14 01:59:46 1
USP Molecular Genetics and Bioinformatics Laboratory
 
Resource Report
Resource Website
1+ mentions
USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) USP Molecular Genetics and Bioinformatics Laboratory laboratory portal, data or information resource, organization portal, portal Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory. genetics, bioinformatics, data mining, genome, gene has parent organization: University of Sao Paulo; Sao Paulo; Brazil THIS RESOURCE IS NO LONGER IN SERVICE nlx_149158 SCR_000605 University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory, USP Laboratorio de Genetica Molecular e Bioinformatica, University of Sao Paulo Molecular Genetics and Bioinformatics Laboratory, USP Molecular Genetics Bioinformatics Laboratory, USP Molecular Genetics and Bioinformatic Laboratory 2026-02-14 01:59:47 1
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility
 
Resource Report
Resource Website
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) core facility, analysis service resource, production service resource, service resource, access service resource Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations. affymetrix, array, PCPGM, gene, expression, data, analysis, service is listed by: Eagle I
has parent organization: Harvard University; Cambridge; United States
THIS RESOURCE IS NO LONGER IN SERVICE nlx_156324 http://www.partners.org/researchcores/trash/bioinformatics_HPCGG.html SCR_000882 PCPGM, bioinformatics, The Partners HealthCare Center for Personalized Genetic Medicine 2026-02-14 01:59:51 0
Yandell Lab Portal
 
Resource Report
Resource Website
Yandell Lab Portal (RRID:SCR_000807) data processing software, portal, laboratory portal, data or information resource, data analysis software, organization portal, software application, software resource Sequenced genomes contain a treasure trove of information about how genes function and evolve. Getting at this information, however, is challenging and requires novel approaches that combine computer science and experimental molecular biology. My lab works at the intersection of both domains, and research in our group can be summarized as follows: generate hypotheses concerning gene function and evolution by computational means, and then test these hypotheses at the bench. This is easier said than done, as serious barriers still exist to using sequenced genomes and their annotations as starting points for experimental work. Some of these barriers lie in the computational domain, others in the experimental. Though challenging, overcoming these barriers offers exciting training opportunities in both computer science and molecular genetics, especially for those seeking a future at the intersection of both fields. Ongoing projects in the lab are centered on genome annotation and comparative genomics; exploring the relationships between sequence variation and human disease; and high-throughput biological image analysis. Current software tools available: VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. MAKER 2 (updated 01-16-2012) MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. RepeatRunner RepeatRunner is a CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements. Because RepeatMasker identifies repeats by means of similarity to a nucleotide library of known repeats, it often fails to identify highly divergent repeats and divergent portions of repeats, especially near repeat edges. To remedy this problem, RepeatRunner uses BLASTX to search a database of repeat encoded proteins (reverse transcriptases, gag, env, etc...). Because protein homologies can be detected across larger phylogenetic distances than nucleotide similarities, this BLASTX search allows RepeatRunner to identify divergent protein coding portions of retro-elements and retro-viruses not detected by RepeatMasker. RepeatRunner merges its BLASTX and RepeatMasker results to produce a single, comprehensive XML-based output. It also masks the input sequence appropriately. In practice RepeatRunner has been shown to greatly improve the efficacy of repeat identifcation. RepeatRunner can also be used in conjunction with PILER-DF - a program designed to identify novel repeats - and RepeatMasker to produce a comprehensive system for repeat identification, characterization, and masking in the newly sequenced genomes. CGL CGL is a software library designed to facilitate the use of genome annotations as substrates for computation and experimentation; we call it CGL, an acronym for Comparitive Genomics Library, and pronounce it Seagull. The purpose of CGL is to provide an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations. software, gene, genome annotation, human has parent organization: University of Utah; Utah; USA
is parent organization of: VAAST
PMID:21700766
PMID:21700266
PMID:21325948
PMID:21347285
nlx_144364 SCR_000807 2026-02-14 01:59:50 0
ROSTLAB
 
Resource Report
Resource Website
1+ mentions
ROSTLAB (RRID:SCR_000792) group A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical has parent organization: Columbia University; New York; USA
is parent organization of: PredictNLS
is parent organization of: SNPdbe
NLM LM007329;
NLM GM50291
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-31417 http://cubic.bioc.columbia.edu/services/disis SCR_000792 Rost Group 2026-02-14 01:59:50 1
Functional Annotation of the Mammalian Genome
 
Resource Report
Resource Website
10+ mentions
Functional Annotation of the Mammalian Genome (RRID:SCR_000788) FANTOM portal, consortium, data or information resource, organization portal, database International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN. mammal, genome, isoform, human, gene, transcriptome, regulatory network, FASEB list is related to: CAGE Basic Viewer for Mus musculus
is related to: RIKEN integrated database of mammals
has parent organization: RIKEN Brain Science Institute
NIMH MH062261 PMID:20211142
PMID:33211864
nif-0000-30552 http://fantom.gsc.riken.jp SCR_000788 Functional Annotation of the Mammalian Genome, FANTOM, Functional Annotation of the Mammalian Genome (FANTOM) 2026-02-14 01:59:50 43
Kyoto Encyclopedia of Genes and Genomes Expression Database
 
Resource Report
Resource Website
1000+ mentions
Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) KEGG Expression Database data repository, storage service resource, data or information resource, service resource, database Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community. encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystis, FASEB list is listed by: LabWorm
is affiliated with: KEGG
has parent organization: Kyoto University; Kyoto; Japan
PMID:9847135
PMID:10592173
Free, Available for download, Freely available r3d100011570, nif-0000-21234 https://doi.org/10.17616/R3792T SCR_001120 Kyoto Encyclopedia of Genes and Genomes Expression Database 2026-02-14 01:59:54 1274
sim4cc
 
Resource Report
Resource Website
sim4cc (RRID:SCR_001204) data processing software, alignment software, software application, software resource, image analysis software Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Johns Hopkins University; Maryland; USA
NSF CLS20163A;
Sloan Research Fellowship ;
NLM R01 LM006845
PMID:19429899 Free, Available for download, Freely available biotools:sim4cc, OMICS_02145 https://bio.tools/sim4cc SCR_001204 2026-02-14 01:59:57 0

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