Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Polyester Resource Report Resource Website 100+ mentions |
Polyester (RRID:SCR_003602) | software application, data processing software, data analysis software, software resource, simulation software | An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code | standalone software, unix/linux, mac os x, windows, r, rna-seq | is listed by: OMICtools | OMICS_04272 | SCR_003602 | 2026-02-16 09:46:09 | 487 | ||||||||||
|
EGAPP Resource Report Resource Website 1+ mentions |
EGAPP (RRID:SCR_004189) | EGAPP | data or information resource, topical portal, portal | Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team. | genetic test, genomics, clinical, genomic technology, evaluation, public health |
is listed by: OMICtools has parent organization: Centers for Disease Control and Prevention |
OMICS_01538 | SCR_004189 | Evaluation of Genomic Applications in Practice and Prevention (EGAPP), Evaluation of Genomic Applications in Practice and Prevention | 2026-02-16 09:46:17 | 1 | ||||||||
|
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 | |||||||
|
libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | software application, software resource, simulation software | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | 2026-02-16 09:48:41 | 11 | ||||||
|
PubMed Resource Report Resource Website 10000+ mentions |
PubMed (RRID:SCR_004846) | data or information resource, database, bibliography | Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut. | biomedical, literature, publication, open, access, bibliography, gold standard |
is used by: Knowledgebase for Addiction Related Genes is used by: Drug Related Gene Database is used by: ChannelPedia is used by: Molecular Imaging and Contrast Agent Database is used by: Colwiz is used by: Nowomics is used by: PINT is listed by: OMICtools is listed by: FORCE11 is listed by: LabWorm is related to: Chilibot: Gene and Protein relationships from MEDLINE is related to: ImpactStory is related to: Automated recognition of brain region mentions in neuroscience literature. is related to: Information Hyperlinked Over Proteins is related to: PubMed Central is related to: PIE the search is related to: Anne O'Tate is related to: PubBrain is related to: Europe PubMed Central is related to: ResearchGate is related to: CBioC is related to: CiteAb is related to: LitInspector is related to: RefMED is related to: Pubmed Commons is related to: iBIOFind is related to: Ensembl Variation is related to: MEDLINE is related to: XplorMed is related to: Linked Neuron Data is related to: NCBI Structure is related to: MeSH is related to: MEDLINE is related to: EBIMed is related to: Coremine Medical is related to: NIF Literature is related to: GoPubMed is related to: Integrated Auto-Extracted Annotation is related to: Polbase is related to: Integrated Manually Extracted Annotation is related to: DaTo is related to: NIF Registry Automated Crawl Data has parent organization: NCBI works with: Open Regulatory Annotation Database works with: rentrez |
NLM | Free, Freely available | nlx_82958, OMICS_01195 | http://www.force11.org/node/4652 http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed |
SCR_004846 | Pub Med | 2026-02-16 09:46:31 | 98390 | ||||||
|
Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | software application, software resource, simulation software | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
EPSRC/MRC Doctoral Training Centre studentship ; BBSRC |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | 2026-02-16 09:48:58 | 23 | ||||||
|
Glide Resource Report Resource Website 10+ mentions |
Glide (RRID:SCR_000187) | Glide | software application, software resource, simulation software | Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening. | ligand, receptor, docking, computation, virtual, screening, drug, discovery |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Ligprep |
PMID:18428795 | Restricted | OMICS_01601 | SCR_000187 | 2026-02-16 09:45:12 | 15 | |||||||
|
Psort Resource Report Resource Website 100+ mentions |
Psort (RRID:SCR_007038) | PSORT | software application, data or information resource, topical portal, production service resource, data processing software, data analysis software, analysis service resource, service resource, software resource, data analysis service, portal, data set | Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses. | subcellular, localization, prediction, gram, gram-positive, gram-negative, sequence, fasta, protein, protein localization, cell, motif, profile, amino acid, subcellular localization |
is listed by: OMICtools is related to: PSORT II has parent organization: Simon Fraser University; British Columbia; Canada |
OMICS_01634, nif-0000-31883 | http://psort.hgc.jp/ | SCR_007038 | Psort.org, PSORT: Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences | 2026-02-17 10:01:11 | 209 | |||||||
|
ProDom Resource Report Resource Website 100+ mentions |
ProDom (RRID:SCR_006969) | ProDom | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | Comprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | set, protein, domain, family, automatically, generated, UniProt, database, homologous, sequence, compare, FASEB list |
is listed by: OMICtools is related to: UniProt is related to: InterPro has parent organization: PRABI |
‘Programme de Bio-Informatique InterOrganismes ; Re´seau des Ge´nopoles ; European Union |
PMID:15608179 PMID:12230033 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01698, nif-0000-03342 | http://prodom.prabi.fr/prodom/current/html/home.php | SCR_006969 | 2026-02-17 10:01:11 | 352 | |||||
|
RTPrimerDB- The Real-Time PCR and Probe Database Resource Report Resource Website 10+ mentions |
RTPrimerDB- The Real-Time PCR and Probe Database (RRID:SCR_007106) | RTPrimerDB | storage service resource, data or information resource, database, service resource, data repository | Database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridization Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimization, and to introduce a certain level of uniformity and standardization among different laboratories. Researchers are encouraged to submit their validated primer and probe sequence, so that other users can benefit from their expertise. The database can be queried using the official gene name or symbol, Entrez or Ensembl Gene identifier, SNP identifier, or oligonucleotide sequence. Different options make it possible to restrict a query to a particular application (Gene Expression Quantification/Detection, DNA Copy Number Quantification/Detection, SNP Detection, Mutation Analysis, Fusion Gene Quantification/Detection, Chromatin immunoprecipitation (ChIP)), organism (Human, Mouse, Rat, and others) or detection chemistry. | primer, probe, sequence, real-time pcr, gene, assay, real-time pcr assay, FASEB list |
is listed by: OMICtools has parent organization: Ghent University; Ghent; Belgium |
PMID:18948285 PMID:16381959 PMID:12519963 |
Public, The community can contribute to this resource | nif-0000-03431, OMICS_02322 | SCR_007106 | 2026-02-17 10:01:03 | 48 | |||||||
|
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 | |||
|
BioRAT Resource Report Resource Website 1+ mentions |
BioRAT (RRID:SCR_007099) | BioRAT | text extraction software, software application, software resource, text-mining software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. An information extraction (IE) tool specifically designed to perform biomedical IE and which is able to locate and analyze both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE. | information extraction, search engine, biomedical, abstract, full-length paper |
is listed by: OMICtools is related to: Comparative Toxicogenomics Database (CTD) has parent organization: University College London; London; United Kingdom |
PMID:15231534 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_013452, nif-0000-21061, OMICS_01175 | SCR_007099 | Biological Research Assistant for Text mining | 2026-02-17 10:01:10 | 1 | ||||||
|
YM500 Resource Report Resource Website |
YM500 (RRID:SCR_007429) | YM500 | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | An Integrative small RNA Sequencing database for miRNA research and provides an integrative web interface for miRNA quantification, isomiR identification, arm switching discovery, and, most of all, novel miRNA predictions. |
is listed by: OMICtools has parent organization: National Yang-Ming University; Taipei; Taiwan |
OMICS_00386 | SCR_007429 | YM500 miR-Seq Database | 2026-02-17 10:01:15 | 0 | |||||||||
|
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 | |||||
|
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 | ||||||
|
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 | |||||||
|
FigTree Resource Report Resource Website 10000+ mentions |
FigTree (RRID:SCR_008515) | data visualization software, data processing software, software application, software resource | A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST. | data visualization software, graphical viewer, phylogenetic tree, annotate |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Edinburgh; Scotland; United Kingdom |
OMICS_04268, nif-0000-30567 | https://sources.debian.org/src/figtree/ | SCR_008515 | FigTree | 2026-02-17 10:01:22 | 11323 | ||||||||
|
Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | software application, web application, data processing software, data analysis software, software resource, sequence analysis software | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-02-17 10:01:14 | 3542 | |||||
|
Qvalue Resource Report Resource Website 10+ mentions |
Qvalue (RRID:SCR_001073) | data analysis software, software application, data processing software, software resource | R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining. | p value, false positive, null hypothesis, genomics, brain imaging, astrophysics, data mining, r, visualization |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00624 | https://github.com/jdstorey/qvalue | SCR_001073 | 2026-02-17 09:59:35 | 31 | ||||||||
|
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 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
