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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.

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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
Atlas of Genetics and Cytogenetics in Oncology and Haematology
 
Resource Report
Resource Website
10+ mentions
Atlas of Genetics and Cytogenetics in Oncology and Haematology (RRID:SCR_007199) data or information resource, database, atlas Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics. gene, cytogenetic, cancer, cancer research, genomic, online journal, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
PMID:23161685 Freely available, Available to the scientific community nif-0000-30129, biotools:atlasgeneticsoncology https://bio.tools/atlasgeneticsoncology SCR_007199 Genetics and Cytogenetics Atlas 2026-02-16 09:46:54 38
SimSeq
 
Resource Report
Resource Website
10+ mentions
SimSeq (RRID:SCR_006947) SimSeq software application, software resource, simulation software An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
Free biotools:simseq, OMICS_00258 https://bio.tools/simseq SCR_006947 2026-02-16 09:46:50 29
RAST Server
 
Resource Report
Resource Website
500+ mentions
RAST Server (RRID:SCR_014606) RAST production service resource, service resource A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools is listed by: Human Microbiome Project
is listed by: Debian
is listed by: bio.tools
National Science Foundation 0850546;
NIAID contract HHSN272200900040C
PMID:18261238 Free for the scientific community, Login required biotools:theseed https://bio.tools/theseed SCR_014606 Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server 2026-02-16 09:48:35 907
oligo
 
Resource Report
Resource Website
1000+ mentions
oligo (RRID:SCR_015729) software application, data processing software, data analysis software, source code, software resource Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ;
NCRR R01RR021967;
NHGRI P41HG004059
PMID:20688976 Free, Available for download, Runs on Mac OS, Runs on Windows biotools:oligo https://bio.tools/oligo SCR_015729 oligo package 2026-02-16 09:48:56 1749
NanoSim
 
Resource Report
Resource Website
10+ mentions
NanoSim (RRID:SCR_018243) software application, software resource, simulation software Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software. Nanopore sequence read, sequence simulator, Oxford Nanopore Technology, next generation sequencing, long nanopore read, genome assembly, mutation detection, bio.tools, bio.tools is listed by: Debian
is listed by: bio.tools
NHGRI R01 HG007182;
Genome Canada ;
Genome British Columbia ;
British Columbia Cancer Foundation ;
University of British Columbia
DOI:10.1093/gigascience/gix010 Free, Available for download, Freely available biotools:trans-nanosim, biotools:nanosim https://www.bcgsc.ca/resources/software/nanosim
https://bio.tools/nanosim
https://bio.tools/Trans-NanoSim
SCR_018243 2026-02-16 09:49:27 18
epitopepredict
 
Resource Report
Resource Website
1+ mentions
epitopepredict (RRID:SCR_019221) software application, software resource, simulation software Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported. Protein sequence, MHC binding prediction, whole genomes, multiple target MHC allele, epitope prediction, bio.tools is listed by: bio.tools
is listed by: Debian
Free, Available for download, Freely available biotools:epitopepredict https://epitopepredict.readthedocs.io/en/latest/
https://bio.tools/epitopepredict
SCR_019221 2026-02-16 09:49:39 2
variancePartition
 
Resource Report
Resource Website
50+ mentions
variancePartition (RRID:SCR_019204) software application, data processing software, data analytics software, data analysis software, software resource Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools is listed by: Bioconductor
is listed by: bio.tools
is listed by: Debian
is related to: CRAN
NHLBI U01 HL107388;
Icahn School of Medicine at Mount Sinai
PMID:27884101 Free, Available for download, Freely available biotools:variancepartition https://bio.tools/variancepartition SCR_019204 2026-02-16 09:49:39 52
MP3 tool
 
Resource Report
Resource Website
1+ mentions
MP3 tool (RRID:SCR_019282) software application, software resource, simulation software Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools is listed by: bio.tools
is listed by: Debian
Institutional Research Fund of IISER Bhopal PMID:24736651 THIS RESOURCE IS NO LONGER IN SERVICE biotools:mp3 https://bio.tools/mp3 SCR_019282 MP3 2026-02-16 09:49:42 2
UTRdb/UTRsite
 
Resource Report
Resource Website
10+ mentions
UTRdb/UTRsite (RRID:SCR_005868) data or information resource, topical portal, portal UTRdb/UTRsite is a portal to other databases, including Nucleotide Sequence Databases, Protein Sequence Databases, other Sequence databanks, Untranslated Nucleotide Sequence Databases, Mitochondrial Databases, Mutation Databases, and others. The site also allows users to start long-term permanent projects or just to do quick searches, depending on the user''s needs. bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
biotools:utrdb, nif-0000-03619 https://bio.tools/utrdb http://bighost.area.ba.cnr.it/srs6/ SCR_005868 UTRdb/UTRsite 2026-02-16 09:46:41 40
WSsas - Web Service for the SAS tool
 
Resource Report
Resource Website
WSsas - Web Service for the SAS tool (RRID:SCR_007051) WSsas data access protocol, web service, software resource SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum. The web service is aimed to facilitate the use of the SAS tool when having a huge number of queries. Currently, the web service provides annotation for binding sites (to ligand, metal or nucleic acid), catalytic residues and amino acids related to protein-protein interactions. gold standard, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: SAS - Sequence Annotated by Structure
has parent organization: European Bioinformatics Institute
nlx_18182, biotools:wssas https://bio.tools/wssas SCR_007051 Web Service for the SAS tool 2026-02-17 10:01:02 0
CD-HIT
 
Resource Report
Resource Website
1000+ mentions
CD-HIT (RRID:SCR_007105) CD-HIT software application, source code, software resource, data processing software THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. cluster, protein, sequence, classification, domain, analysis, nucleotide sequence, dna, protein sequence, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
has parent organization: University of California at San Diego; California; USA
has parent organization: Google Code
is parent organization of: CD-HIT-OTU
NCRR 1R01RR025030 PMID:20053844
PMID:16731699
DOI:10.1093/bioinformatics/btl158
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_05157, biotools:cd-hit, nif-0000-30240 http://cd-hit.org
https://code.google.com/p/cdhit/
https://bio.tools/cd-hit
https://sources.debian.org/src/cd-hit/
http://bioinformatics.ljcrf.edu/cd-hi/
SCR_007105 CD-HIT Program 2026-02-17 10:01:12 3203
Expression Database in 4D
 
Resource Report
Resource Website
1+ mentions
Expression Database in 4D (RRID:SCR_007066) 4DXpress storage service resource, data or information resource, database, service resource, data repository This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data. genes, anatomical structures, developmental stage, microarray data, species, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: European Molecular Biology Laboratory
European Molecular Biology Laboratory; Heidelberg; Germany PMID:17916571 nif-0000-02524, biotools:4dxpress https://bio.tools/4dxpress SCR_007066 4DXpress Database 2026-02-17 10:01:00 1
Chromosome 7 Annotation Project
 
Resource Report
Resource Website
10+ mentions
Chromosome 7 Annotation Project (RRID:SCR_007134) Chromosome 7 Annotation Project storage service resource, data or information resource, database, service resource, data repository Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed. duplication, gene expression, family, fish, gene, gene annotation, genome, breakpoint, chromosome, chromosome 7, clinical, deletion, disease, dna sequence, human, insertion, inversion, polymorphism, rearrangement, segmental duplication, snp, translocation, annotation, data analysis service, blat, cosmid, bac, yac, biomaterial supply resource, malignant, non malignant, bio.tools is listed by: One Mind Biospecimen Bank Listing
is listed by: Debian
is listed by: bio.tools
PMID:12690205 Free, (Genomic clones) nif-0000-03550, biotools:chr7, r3d100012136 https://bio.tools/chr7
https://doi.org/10.17616/R3VP9V
SCR_007134 The Chromosome 7 Annotation Project, Chromosome 7 Annotation Project 2026-02-17 10:01:12 13
VISTA Enhancer Browser
 
Resource Report
Resource Website
100+ mentions
VISTA Enhancer Browser (RRID:SCR_007973) VISTA Enhancer Browser storage service resource, data or information resource, database, service resource, data repository Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
is related to: NIF Data Federation
is related to: One Mind Biospecimen Bank Listing
is related to: OMICtools
has parent organization: Lawrence Berkeley National Laboratory
American Heart Association ;
NIDCR ;
NHLBI HL066681;
NHGRI HG003988;
DOE contract DE-AC02-05CH11231;
NINDS NS062859;
DOE DE020060
PMID:17130149 Free, Freely available nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser https://bio.tools/vista_enhancer_browser SCR_007973 2026-02-17 10:01:09 233
T1DBase
 
Resource Report
Resource Website
100+ mentions
T1DBase (RRID:SCR_007959) storage service resource, data or information resource, resource, database, service resource, data repository THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data. genetics, beta cell, gene, variant, region, genomics, gene expression, genome-wide association study, data analysis service, bio.tools is used by: NIF Data Federation
is used by: NIDDK Information Network (dkNET)
is listed by: NIDDK Information Network (dkNET)
is listed by: Debian
is listed by: bio.tools
is related to: dkCOIN
has parent organization: University of Cambridge; Cambridge; United Kingdom
Type 1 diabetes. Diabetes Wellcome Trust ;
NIDDK ;
Juvenile Diabetes Research Foundation
PMID:20937630 THIS RESOURCE IS NO LONGER IN SERVICE. nif-0000-03531, biotools:t1dbase https://bio.tools/t1dbase SCR_007959 T1DBase - Type 1 Diabetes Database 2026-02-17 10:01:05 145
QIIME
 
Resource Report
Resource Website
10000+ mentions
QIIME (RRID:SCR_008249) data analysis software, software application, data processing software, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics. microbiome, microbial community, sequence data, data analysis software, bio.tools is used by: SortMeRNA
is used by: Nephele
is listed by: OMICtools
is listed by: Human Microbiome Project
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
has parent organization: University of Colorado Boulder; Colorado; USA
DOI:10.1038/nmeth.f.303 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01118, SCR_011948, OMICS_01521, biotools:qiime https://bio.tools/qiime SCR_008249 Quantitative Insights Into Microbial Ecology 2026-02-17 10:01:12 11036
dbEST
 
Resource Report
Resource Website
100+ mentions
dbEST (RRID:SCR_008132) storage service resource, data or information resource, database, service resource, data repository Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms. data, sequence, single, pass, cDNA, express, tag, bio.tools, gold standard is listed by: Debian
is listed by: bio.tools
has parent organization: NCBI
PMID:8401577 biotools:dbest, nif-0000-20937, r3d100010648 http://www.ncbi.nlm.nih.gov/dbEST/
https://bio.tools/dbest
https://doi.org/10.17616/R3FG8P
SCR_008132 database Expressed Sequence Tag (EST), database Expressed Sequence Tag 2026-02-17 10:01:06 179
ActiveDriver
 
Resource Report
Resource Website
10+ mentions
ActiveDriver (RRID:SCR_008104) ActiveDriver software application, data processing software, data analysis software, software resource, sequence analysis software A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications. Protein sequence variation, variation interpretation, protein sequence, protein post-translational signaling modifications, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
Free, Available for download, Freely available biotools:ActiveDriver, OMICS_00140 http://reimandlab.org/software/activedriver/
https://cran.r-project.org/web/packages/ActiveDriver/ActiveDriver.pdf
https://bio.tools/ActiveDriver
SCR_008104 2026-02-17 10:01:06 25
G protein receptor interaction feature finding instrument
 
Resource Report
Resource Website
10+ mentions
G protein receptor interaction feature finding instrument (RRID:SCR_008343) resource, production service resource, analysis service resource, service resource Griffin (G-protein-receptor interacting feature finding instrument) is a high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight. This system consists of two parts: 1) HMM section using family specific multiple alignment of GPCRs, 2) SVM section using physico-chemical feature vectors in GPCR sequence. G-protein coupled receptors (GPCR), which is composed of seven transmembrane helices, play a role as interface of signal transduction. The external stimulation for GPCR, induce the coupling with G-protein (Gi/o, Gq/11, Gs, G12/13) followed by different kinds of signal transduction to inner cell. About half of distributed drugs are intending to control this GPCR - G-protein binding system, and therefore this system is important research target for the development of effective drug. For this purpose, it is necessary to monitor, effectively and comprehensively, of the activation of G-protein by identifying ligand combined with GPCR. Since, at present, it is difficult to construct such biochemical experiment system, if the answers for experimental results can be prepared beforehand by using bioinformatics techniques, large progress is brought to G-protein related drug design. Previous works for predicting GPCR-G protein coupling selectivity are using sequence pattern search, statistical models, and HMM representations showed high sensitivity of predictions. However, there are still no works that can predict with both high sensitivity and specificity. In this work we extracted comprehensively the physico-chemical parameters of each part of ligand, GPCR and G-protein, and choose the parameters which have strong correlation with the coupling selectivity of G-protein. These parameters were put as a feature vector, used for GPCR classification based on SVM. drug, alignment, biochemical, bioinformatic, coupling, gpcr, g-protein, helix, instrument, interface, ligand, molecular, pattern, physico-chemical, receptor interacting, sequence, signal transduction, stimulation, svm, system, technique, transmembrane, weight, instrument, equipment, hardware, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Computational Biology Research Center Core Facility
National Institute of Advanced Industrial Science and Technology nif-0000-25210, biotools:griffin https://bio.tools/griffin SCR_008343 Griffin 2026-02-17 10:01:13 19
ToppCluster
 
Resource Report
Resource Website
100+ mentions
ToppCluster (RRID:SCR_001503) ToppCluster resource, production service resource, analysis service resource, service resource, data analysis service A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: GenitoUrinary Development Molecular Anatomy Project
is related to: ToppGene Suite
NIDDK 1U01DK70219;
NIDDK P30DK078392;
NCRR U54 RR025216;
NIDCR U01DE020049
PMID:20484371 Free OMICS_02225, nlx_152801, biotools:toppcluster https://bio.tools/toppcluster SCR_001503 ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems 2026-02-17 09:59:40 144

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