Searching the RRID Resource Information Network
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 | |||||||||||||
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Lasker Foundation Resource Report Resource Website 1+ mentions |
Lasker Foundation (RRID:SCR_005114) | Lasker Foundation | institution | The Albert and Mary Lasker Foundation and its programs are dedicated to the support of biomedical research toward conquering disease, improving human health and extending life. The Foundation''s mission is to foster the prevention and treatment of disease and disabilities by honoring excellence in basic and clinical science, by educating the public, and by advocating for support of medical research. The Lasker Awards The Lasker Foundation''s Awards Program recognizes the contributions of scientists, physicians, and public servants who have made major advances in the understanding, diagnosis, treatment, cure or prevention of human disease. Other Programs Although the Lasker Foundation is not a grant-giving organization, it does support select initiatives that raise awareness of medical discoveries and their benefits to human health, and that increase support for the medical science enterprise. These initiatives have included study groups, Congressional briefings, innovative web-based programs, educational forums, and scholarly studies. | biomedical, award, research, basic science, clinical science | ISNI: 0000 0000 9598 7178, nlx_144121, Crossref funder ID: 100009577, grid.480586.7 | https://ror.org/05fcw6535 | SCR_005114 | Albert and Mary Lasker Foundation, Albert Mary Lasker Foundation | 2026-02-14 02:00:51 | 2 | ||||||||
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IsoformEx Resource Report Resource Website 1+ mentions |
IsoformEx (RRID:SCR_005235) | software resource | Software that estimates transcript expression levels and gene expression levels from mRNA-Seq data. Technically speaking, IsoformEx parses bowtie alignment files in a project directory (e.g. ~yourid/isoformex/xxx, where xxx is the project name) and generates two files: (1) xxx/xxx_transcript_1.txt: expression levels of all transcripts, (2) xxx/xxx_gene_1.txt: expression levels of all genes. |
is listed by: OMICtools has parent organization: University of Pennsylvania; Philadelphia; USA |
Free for academic use, Commercial use with permission | OMICS_01260 | SCR_005235 | IsoformEx: Isoform level gene expression estimation using non-negative least squares from mRNA-Seq data | 2026-02-14 02:00:53 | 2 | |||||||||
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BioPortfolio Resource Report Resource Website 1+ mentions |
BioPortfolio (RRID:SCR_005230) | BioPortfolio | job resource, blog, portal, data or information resource, narrative resource, database | BioPortfolio is a leading news, information and knowledge resource covering the global life science industries impacted on by biotechnology. The site aims to provide the lay person, the researcher and the management executive with a single location to source core information on specific bio-related topics, to collate relevant data associated with each topic and to point the user to relevant knowledge resources. We publish up to the minute news (see biotechnology news categories) and regularly update content across our information databases. BioPortfolio promotes and sells market research and management reports from 30+ publishers. In addition our unique corporate database lists 40,000+ companies and organizations. BioPortfolio aims to bring together high quality information about marketed drugs - medication and relevant clinical trials, research papers and recent news from PubMed, ClinicalTrials.gov, and DailyMed. Additionally, resources include biotech, pharma and medical job listings. When the BioPortfolio site was launched in February 1997 the company aimed to provide a global free-to-use resource with defined aims and mission statement: to meet the increasing demand of consumers, scientists, investors, commerce and government for timely, accurate and commercially useful information and intelligence on biotechnology companies, technologies and products world-wide. Driven by the success of the site we have made major investments and improvements to enhance our content and to apply the latest web technologies to improve functionality and site utility. We believe this unique depth and breadth of content is supporting individuals, organizations and policy-makers to become more aware of the role of biotechnology on the global economy. With 97,000 users visiting the site more than once per month we are confident that we are providing information our users need. We hope you the users find the site of value for both personal and professional reasons. Please enjoy this free resource and email your comments! | news, information, knowledge, life science, biotechnology, pubmed, corporate, clinical trial, drug, career, pharmaceutical, healthcare, medicine, clinical, industry |
is used by: NIF Data Federation is used by: Integrated Blogs |
For personal non-commercial use only | nlx_144235 | SCR_005230 | 2026-02-14 02:01:05 | 1 | ||||||||
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aldex Resource Report Resource Website 10+ mentions |
aldex (RRID:SCR_005110) | aldex | software resource | RNA-seq tool that uses the Dirichlet distribution and a transformation to identify genes that exhibit small within-condition and large between-condition variance. | transcriptome, meta-transcriptome |
is listed by: OMICtools is related to: ALDEx2 |
GNU General Public License, v3 | OMICS_01297 | SCR_005110 | aldex: ANOVA-like RNA-seq analysis | 2026-02-14 02:00:51 | 12 | |||||||
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ABSOLUTE Resource Report Resource Website 100+ mentions |
ABSOLUTE (RRID:SCR_005198) | ABSOLUTE | software resource | Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles. |
is listed by: OMICtools has parent organization: Broad Institute |
Cancer, Normal | PMID:22544022 | Account required | OMICS_00217 | SCR_005198 | 2026-02-14 02:01:03 | 263 | |||||||
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VARIANT Resource Report Resource Website 1000+ mentions |
VARIANT (RRID:SCR_005194) | VARIANT | data processing software, data analysis service, analysis service resource, data analysis software, production service resource, service resource, software application, software resource | Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line |
is listed by: OMICtools has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Science and Innovation BIO2011-27069 | PMID:22693211 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00193 | SCR_005194 | Variant effect, VARIant ANalysis Tool | 2026-02-14 02:00:50 | 1366 | |||||
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SNPdbe Resource Report Resource Website 1+ mentions |
SNPdbe (RRID:SCR_005190) | SNPdbe | data repository, storage service resource, data or information resource, service resource, database | A database to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. It currently covers over 155,000 protein sequences which come from more than 2,600 organisms. Overall more than one million single amino acid substitutions (SAASs) are referenced consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts. SNPdbe offers the following pieces of information (if available) on each SAAS: * Experimentally derived functional and structural impact * Predicted functional effect * Associated disease * Average heterozygosity * Experimental evidence of the nsSNP * Evolutionary conservation of wildtype and mutant amino acid * Link-outs to external databases A convenient webinterface to query SAASs on the following levels is offered: * Protein and gene identifiers and keywords * Disease keywords * Protein sequence on different sequence identity thresholds * Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence They offer the possibility to submit protein sequences along with experimentally substantiated mutations in order to predict their functional effect and inclusion into our database. | single amino acid substitution, protein variant, protein, variant, protein sequence, natural variant, mutagenesis, sequencing, mutation |
is listed by: OMICtools has parent organization: ROSTLAB |
PMID:22210871 | Free for academic use, Non-commercial, Commercial use with permission, The community can contribute to this resource | OMICS_00185 | SCR_005190 | SNPdbe - nsSNP database of functional effects, nsSNP database of functional effects | 2026-02-14 02:00:52 | 4 | ||||||
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CTSAconnect Resource Report Resource Website |
CTSAconnect (RRID:SCR_005225) | CTSAconnect | ontology, knowledge environment, data or information resource, source code, service resource, controlled vocabulary, software resource, narrative resource, standard specification | THIS RESOURCE IS NO LONGER IS SERVICE. Documented on December 5th, 2022. Semantic framework to integrate information about research activities, clinical activities, and scientific resources to facilitate the production and consumption of Linked Open Data about investigators, physicians, biomedical research resources, services, and clinical activities. The goal is to enable software to consume data from multiple sources and allow the broadest possible representation of researchers'''' and clinicians'''' activities and research products. Current research tracking and networking systems rely largely on publications, but clinical encounters, reagents, techniques, specimens, model organisms, etc., are equally valuable for representing expertise. CTSAConnect will provide linkage between semantic representations of a wide range of clinical and research data using controlled vocabularies mapped to the Unified Medical Language System (UMLS) as a bridge between the two subject areas. The data sources include data from Medicaid, hospital billing systems, CTSAShareCenter, and other CTSA resource data, eagle-i and VIVO. It allows institutions to leverage existing tools and data sources by making the information they contain more discoverable and easier to integrate. For instance, with the ISF, researchers can be characterized by organizational affiliations, grant and project participation, research resources that they have generated, and publications that they have (co)-authored. Clinicians can be characterized by training and credentials, by clinical research topic, and by the kinds of procedures and specialization that can be inferred from encounter data. LOD refers to data that has been given a specific Uniform Resource Identifier (URI), for the purpose of sharing and linking data and information on the Semantic Web. While a large amount of data is published as LOD, there remains a significant gap in the representation of research resources and clinical expertise. Researchers can be characterized by the organization to which they belong, the grants and research in which they have participated, the research topics and research resources (reagents, biospecimens, animal models) they have generated, as well as the publications they have (co)-authored. Clinician profiles on the other hand, can be defined by their credentials, clinical research topics, and the kinds of procedures and specialization that can be inferred from clinical encounter data. They believe that integrating and relating this diversity of information sources and platforms requires addressing the overlap between research resources and the attributes and activities of researchers and clinicians. CTSAconnect aims to promote integration and discovery of research activities, resources, and clinical expertise. To this end, they will publish their ontologies and LOD via their website, which will also illustrate repeatable methods and examples of how to extract, consume, and utilize this valuable new LOD using freely available tools like VIVO, eagle-i, and Google APIs. CTSAconnect is a collaboration between Oregon Health & Science University, Stony Brook University, Cornell University, Harvard University, University at Buffalo, and the University of Florida, and leverages the work of eagle-i (eagle-i.net), VIVO (vivoweb.org), and ShareCenter (ctsasharecenter.org). | data sharing, clinical, research, semantic framework, linked open data, collaborate |
is related to: Eagle I is related to: VIVO is related to: CTSA ShareCenter is related to: Clinical and Translational Science Awards Consortium is related to: CTSA ShareCenter has parent organization: Oregon Health and Science University; Oregon; USA has parent organization: Harvard University; Cambridge; United States |
Booz Allen Hamilton ; National Center for Advancing Translational Sciences |
THIS RESOURCE IS NO LONGER IS SERVICE | nlx_144228 | SCR_005225 | CTSAconnect: A Linked Open Data approach to represent clinical and research expertise activities and resources, CTSA Connect, Clinical and Translational Science Awards Connect | 2026-02-14 02:01:05 | 0 | ||||||
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qSNP Resource Report Resource Website 10+ mentions |
qSNP (RRID:SCR_005105) | qSNP | software resource | A single nucleotide variant caller optimised for identifying somatic variants in low cellularity cancer samples. |
is listed by: OMICtools has parent organization: University of Queensland; Brisbane; Australia |
Cancer | PMID:24250782 | OMICS_00089 | SCR_005105 | 2026-02-14 02:00:51 | 24 | ||||||||
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Damon Runyon Cancer Research Foundation Resource Report Resource Website 50+ mentions |
Damon Runyon Cancer Research Foundation (RRID:SCR_005106) | Damon Runyon Foundation | institution | The Damon Runyon Cancer Research Foundation funds early career cancer researchers who have the energy, drive and creativity to become leading innovators in their fields. We identify the best young scientists in the nation and support them through four award programs: our Fellowship, Pediatric Cancer Fellowship, Clinical Investigator and Innovation Awards. Damon Runyon awards give young scientists: * Freedom to follow their own ideas, explore new paths and take risks * A prestigious endorsement that attracts further funding, advances their careers and accelerates their research * Guaranteed financial support, sparing them hours applying for grants Since 1946, Damon Runyon has invested more than $240 million in the best young minds in the nation. Our alumni include 11 Nobel Laureates and leaders of major cancer centers across the United States. Many of our 3,300 scientists have gone on to make breakthroughs in the way we prevent, diagnose and treat many forms of cancer. The Damon Runyon Cancer Research Foundation is a registered nonprofit with 501(c)(3) status. | fellowship, grant, cancer | Crossref funder ID: 100001021, grid.453008.a, ISNI: 0000 0004 0508 2172, nlx_144117 | https://ror.org/01gd7b947 | SCR_005106 | 2026-02-14 02:01:04 | 63 | |||||||||
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SAMtools/BCFtools Resource Report Resource Website 500+ mentions |
SAMtools/BCFtools (RRID:SCR_005227) | BCFtools | software resource | Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. | snp, indel, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SAMTOOLS |
DOI:10.1101/090811 | biotools:bcftools, OMICS_13458 | https://bio.tools/bcftools https://sources.debian.org/src/bcftools/ |
SCR_005227 | 2026-02-14 02:01:04 | 904 | |||||||
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MiTie Resource Report Resource Website 1+ mentions |
MiTie (RRID:SCR_005228) | MiTie | software resource | Software framework for simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples. They define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data, and show how to find the optimal solution using Mixed Integer Programming. MiTie can a) take advantage of known transcripts, b) reconstruct and quantify transcripts simultaneously in multiple samples, as well as c) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. | c++, rna-seq, transcript | is listed by: OMICtools | OMICS_01279 | SCR_005228 | MiTie: Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples | 2026-02-14 02:00:53 | 4 | ||||||||
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ORMAN Resource Report Resource Website 1+ mentions |
ORMAN (RRID:SCR_005188) | ORMAN | software resource | A software tool for resolving multi-mappings within an RNA-Seq SAM file. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24130305 | OMICS_01284, biotools:orman | https://bio.tools/orman | SCR_005188 | ORMAN : Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms | 2026-02-14 02:00:50 | 4 | ||||||
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FRCbam Resource Report Resource Website 10+ mentions |
FRCbam (RRID:SCR_005189) | software resource | Software package containing tools to process bam files in order to evaluate and analyze de novo assembly / assemblers and identify Structural Variations suspicious genomics regions. The tools have been already successfully applied in several de novo and resequencing projects. This package contains two tools: # FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers # FindTranslocations: tool to identify chromosomal rearrangements using Mate Pairs | standalone software, sam, bam | is listed by: OMICtools | PMID:23284938 | GNU General Public License, v3 | OMICS_04070 | SCR_005189 | 2026-02-14 02:01:03 | 11 | ||||||||
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University of KwaZulu-Natal; Durban; South Africa Resource Report Resource Website 1+ mentions |
University of KwaZulu-Natal; Durban; South Africa (RRID:SCR_005222) | UKZN | university | University with five campuses in the province of KwaZulu-Natal in South Africa. It was formed on 1 January 2004 after the merger between the University of Natal and the University of Durban-Westville. |
is parent organization of: Africa Centre Biobank is parent organization of: BioAfrica HIV Informatics in Africa is parent organization of: Africa Centre for Health and Population Studies |
nlx_51412, ISNI:0000 0001 0723 4123, Wikidata:Q727516, grid.16463.36, Crossref funder ID:501100004695 | https://ror.org/04qzfn040 | SCR_005222 | University of KwaZulu-Natal, University of KwaZulu Natal | 2026-02-14 02:01:03 | 3 | ||||||||
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SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | data analysis service, analysis service resource, production service resource, service resource, software resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-02-14 02:00:52 | 2 | ||||||
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NGS-SNP Resource Report Resource Website 10+ mentions |
NGS-SNP (RRID:SCR_005182) | NGS-SNP | software resource | A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species. | annotation, snp, sequencing, transcript, genome, reference sequence, indel, annotate, reference chromosome, reference transcript, gene, command-line |
is listed by: OMICtools is related to: Ensembl has parent organization: University of Alberta; Alberta; Canada |
OMICS_00177 | SCR_005182 | 2026-02-14 02:00:50 | 32 | |||||||||
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SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data analysis software, software resource, data processing software, software application | Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells. | small RNAs datasets, ubiquitous miRNA modifications, human embryonic cells, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Spanish Ministry of Health ; CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-02-14 02:01:53 | 30 | ||||||
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Fiber Optic Button Response System Resource Report Resource Website 10+ mentions |
Fiber Optic Button Response System (RRID:SCR_009577) | instrument resource | Instrument that accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact, chemical resistant, medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant?s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed. | eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, response monitoring, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155759 | http://www.nitrc.org/projects/fobrs https://pstnet.com/wp-content/uploads/2021/04/Celeritas-Operator-Manual.pdf |
SCR_009577 | Celeritas Fiber Optic Response System | 2026-02-14 02:01:52 | 22 | ||||||||
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Oregon State University; Oregon; USA Resource Report Resource Website 1+ mentions |
Oregon State University; Oregon; USA (RRID:SCR_009731) | university | Public research university in Corvallis, Oregon. The university currently offers more than 200 undergraduate-degree programs along with a variety of graduate and doctoral degrees. |
is parent organization of: TileQC is parent organization of: AFTOL is parent organization of: CASHX is parent organization of: Chromaseq is parent organization of: Plant Ontology is parent organization of: Plant Ontology is parent organization of: Northern Spalting - Applied Mycology Lab is parent organization of: EnVision Manager is parent organization of: Oregon State University Center for Quantitative Life Sciences Core Facility is parent organization of: Oregon State University Electron Microscopy Core Facility |
Wikidata:Q861888, ISNI:0000 0001 2112 1969, Crossref funder ID:100009612, nlx_87751, grid.4391.f | https://ror.org/00ysfqy60 | SCR_009731 | 2026-02-14 02:01:54 | 1 |
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