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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
G-BLASTN Resource Report Resource Website |
G-BLASTN (RRID:SCR_005062) | G-BLASTN | software resource | A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. | parallel computation 4, blast, alignment, nucleotide, gpu, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BLAST has parent organization: Hong Kong Baptist University; Hong Kong; China has parent organization: SourceForge |
Hong Kong Baptist University; Hong Kong; China FRG2/11-12/158; NVIDIA |
PMID:24463183 | Free | OMICS_02263, biotools:g-blastn | http://sourceforge.net/projects/gblastn/ https://bio.tools/g-blastn |
SCR_005062 | 2026-02-14 02:01:02 | 0 | |||||
|
Classifier for Metagenomic Sequences Resource Report Resource Website 100+ mentions |
Classifier for Metagenomic Sequences (RRID:SCR_004929) | ClaMS | data analysis software, software resource, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned. | metagenome, classification, sequence |
is listed by: OMICtools has parent organization: DOE Joint Genome Institute |
DOE contract DE-AC02-05CH11231 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_005519, nlx_144629, OMICS_01452 | SCR_004929 | 2026-02-14 02:00:46 | 150 | |||||||
|
Stanford Research Institute International Resource Report Resource Website 1+ mentions |
Stanford Research Institute International (RRID:SCR_004926) | SRI | institution | Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977. |
is related to: Stanford University; Stanford; California is parent organization of: BioCyc is parent organization of: NIMH Toxicological Screens of Novel Ligands is parent organization of: Project Halo is parent organization of: EcoCyc is parent organization of: NCANDA: Data Integration Component is parent organization of: SRI24 Atlas: Normal Adult Brain Anatomy is parent organization of: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is parent organization of: MetaCyc |
nif-0000-00235 | SCR_004926 | SRI International, Stanford Research Institute | 2026-02-14 02:00:49 | 2 | |||||||||
|
MethodBox Resource Report Resource Website 1+ mentions |
MethodBox (RRID:SCR_004928) | MethodBox | data repository, storage service resource, community building portal, portal, data set, data or information resource, source code, service resource, software resource | Collaboration environment for sharing variable sets and statistical methods for analysis across social science survey data. MethodBox enables you to browse and download datasets, share methods and scripts, find fellow researchers with similar interests and share your knowledge. MethodBox source available on Google code. Finding the variables you need to support a particular research question can be time consuming. Wading through hundreds of pages of PDF documents, codebooks and metadata and then trying to find the exact column in a huge spreadsheet can be very frustrating. MethodBox gets you to the variables faster and lets you download only the data you need. You can also share your scripts with others to allow them to adopt best practice quicker than before. | variable, survey data, method, script, data sharing, social science | has parent organization: University of Manchester; Manchester; United Kingdom | ESRC | PMID:20841736 | Account required | nlx_89127 | SCR_004928 | 2026-02-14 02:01:02 | 1 | ||||||
|
SLIDE Resource Report Resource Website 10+ mentions |
SLIDE (RRID:SCR_005137) | SLIDE | software resource | Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NIH ; NHGRI HG004695; NHGRI HG005639; NEI EY019094 |
PMID:22135461 | OMICS_01291 | SCR_005137 | sparse linear modeling of RNA-Seq data for isoform discovery and abundance estimation | 2026-02-14 02:00:49 | 32 | |||||||
|
VFS Resource Report Resource Website 1+ mentions |
VFS (RRID:SCR_005138) | VFS | software resource | A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. | ubuntu, debian, high-throughput sequencing, virus, reconstruct, fusion transcript, transcript, integration, fusion, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23314323 | GNU General Public License, v3 | OMICS_00224, biotools:viralfusionseq | https://bio.tools/viralfusionseq | SCR_005138 | ViralFusionSeq, ViralFusionSeq (VFS) | 2026-02-14 02:01:03 | 1 | |||||
|
RetroSeq Resource Report Resource Website 10+ mentions |
RetroSeq (RRID:SCR_005133) | RetroSeq | software resource | A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences. | mobile element insertion, next-gen sequencing, bam, transposable element, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:23233656 | Acknowledgement requested, Open unspecified license | OMICS_11232, OMICS_00120 | SCR_005133 | 2026-02-14 02:00:51 | 45 | |||||||
|
Cloudbreak Resource Report Resource Website |
Cloudbreak (RRID:SCR_005097) | software resource | Software providing a Hadoop-based genomic structural variation (SV) caller for Illumina paired-end DNA sequencing data. It contains a full pipeline for aligning data in the form of FASTQ files using alignment pipelines that generate many possible mappings for every read, in the Hadoop framework. It then contains Hadoop jobs for computing genomic features from the alignments, and for calling insertion and deletion variants from those features. | illumina, mapreduce, insertion, deletion, genomic | is listed by: OMICtools | OMICS_04078 | SCR_005097 | 2026-02-14 02:01:02 | 0 | ||||||||||
|
St. Louis University Alzheimer's Brain Bank Resource Report Resource Website |
St. Louis University Alzheimer's Brain Bank (RRID:SCR_005132) | biomaterial supply resource, material resource, tissue bank, brain bank | A brain bank which provides brain tissue for interdisciplinary research in neurochemical, anatomical, epidemiological and clinical aspects of Alzheimer's disease. It provides brain tissue from Alzheimer's patients and healthy elderly brain donors to investigators who are helping further the understanding of Alzheimer's disease through research. It also gives family members of Alzheimer's patients the opportunity to obtain a confirmed diagnosis through brain autopsy. Through this program, families of individuals with either a clinical diagnosis, or those with suspected Alzheimer's disease, grant permission for a brain autopsy to be performed immediately after death. | brain bank, alzheimer's disease, normal control, dementia, brain tissue, autopsy, healthy donor, material storage repository |
is listed by: One Mind Biospecimen Bank Listing has parent organization: St. Louis University Department of Neurology and Psychiatry has parent organization: Saint Louis University School of Medicine; Missouri; USA |
Alzheimer's disease, Dementia | alz.org | Public, Available to the research community | nlx_144152 | SCR_005132 | SLU Brain Bank, Saint Louis University Alzheimer’s Brain Bank, Saint Louis University Medical Center Alzheimer's Disease Brain Bank | 2026-02-14 02:01:03 | 0 | ||||||
|
MMAPPR Resource Report Resource Website 1+ mentions |
MMAPPR (RRID:SCR_005092) | MMAPPR | software resource | A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants. | mutation, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
PMID:23299975 | Acknowledgement requested | OMICS_01361, biotools:mmappr | https://bio.tools/mmappr | SCR_005092 | Mutation Mapping Analysis Pipeline for Pooled RNA-seq | 2026-02-14 02:01:02 | 7 | |||||
|
Gene Map Annotator and Pathway Profiler Resource Report Resource Website 100+ mentions |
Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) | software resource, data visualization software, data processing software, software application | GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options. | expression, gene, analysis, biological, mapping, microarray, network, pathway, protein, visualization, ontology, proteomics, FASEB list |
has parent organization: University of California at San Francisco; California; USA is parent organization of: MAPPFinder |
Agilent Foundation ; BayGenomics ; NIGMS |
PMID:17588266 | nif-0000-00244 | SCR_005094 | GenMAPP | 2026-02-14 02:01:04 | 211 | |||||||
|
Cereal Plant Development Ontology Resource Report Resource Website |
Cereal Plant Development Ontology (RRID:SCR_005095) | GRO-CPD | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology. | obo |
is listed by: BioPortal is related to: Plant Ontology has parent organization: Gramene |
nlx_157358 | http://www.gramene.org/plant_ontology/ | SCR_005095 | 2026-02-14 02:00:49 | 0 | ||||||||
|
Regions Hospital Alzheimer's Research Center Resource Report Resource Website |
Regions Hospital Alzheimer's Research Center (RRID:SCR_005128) | disease-related portal, data or information resource, portal, topical portal | A national research center that conducts research for Alzheimer's disease, stroke and other nervous system disorders. The mission of the Center is to improve the treatment and prevention of Alzheimer's disease and other neurologic disorders by advancing scientific knowledge through creative and collaborative research. | alzheimer's disease, stroke, nervous system disease, neurodegenerative disease | is parent organization of: Dementia Brain Bank Research Program | Alzheimer's disease, Nervous system disorders | Charitable gifts | Public | nlx_144135 | SCR_005128 | MN Alzheimer's Research Center, Minnesota Alzheimer's Research Center | 2026-02-14 02:01:04 | 0 | ||||||
|
MJ Murdock Charitable Trust Resource Report Resource Website 1+ mentions |
MJ Murdock Charitable Trust (RRID:SCR_005122) | Murdock Trust | institution | The M. J. Murdock Charitable Trust seeks to enrich the quality of life in the Pacific Northwest by providing grants and enrichment programs to non-profit organizations that seek to strengthen the region''s educational, spiritual, and cultural base in creative and sustainable ways. In addition to a special interest in education and scientific research, the Trust partners with a wide variety of organizations that serve the arts, public affairs, health and medicine, human services, leadership development, and persons with disabilities. Eligibility for scientific research grants is limited. Select public research universities and medical institutes located within the five-state region (Pacific Northwest: Alaska, Washington, Oregon, Idaho, Montana) are typically considered for funding. The Trust prefers requests for projects in the natural sciences where the main objective is the acquisition of new knowledge. However, requests for research in engineering and medicine are also eligible. Training students in conducting research is an important consideration. | grant, enrichment program, life science, research, natural science | grid.453269.f, Crossref funder ID: 100000937, nlx_144130 | https://ror.org/02hxgd925 | SCR_005122 | Murdock Charitable Trust, Murdock Trust | 2026-02-14 02:00:49 | 8 | ||||||||
|
National Academy of Sciences Podcasts Resource Report Resource Website |
National Academy of Sciences Podcasts (RRID:SCR_005124) | NAS Podcasts | data or information resource, podcast, narrative resource | Subscribe to the National Academy of Sciences podcasts to learn more about scientists and their work, the latest in research, and key findings of National Research Council reports. * InterViews: InterViews provides first-person accounts of the lives and work of National Academy of Sciences members. In this series of one-on-one conversations, scientists talk about what inspired them to pursue the careers they chose and describe some of the most fascinating aspects of their research. * Science Sessions: The Proceedings of the National Academy of Sciences offers brief, 5-minute, nontechnical conversations with cutting-edge researchers, including members of the National Academy of Sciences, and policymakers as they discuss topics relevant to today''s scientific community. Learn the behind-the-scenes story of work published in PNAS, plus a broad range of scientific news about discoveries that affect the world around us. * News from the National Academies: Listen to the latest news conferences and public briefings on National Research Council and Institute of Medicine reports. * Sounds of Science: This informative and entertaining series puts a spotlight on the high-impact work of the National Research Council. Focusing on a wide range of critical issues in science, engineering, and medicine, these short episodes are a quick and easy way to tune in our key findings and important recommendations. * Cultural Programs: The Cultural Programs of the National Academy of Sciences presents public exhibitions, lectures, and other programs exploring the intersections of art, science, and culture. The podcast features audio recordings of past lectures and other events. * Engineering Innovation: This weekly podcast from the National Academy of Engineering highlights exciting developments in engineering and provides technical context to stories in the news. The 40-second episodes demonstrate how engineers are making an impactin energy, health, the environment, sports, and more. | science, culture, research, engineering, medicine, news, interview |
is used by: NIF Data Federation is related to: Integrated Podcasts has parent organization: National Academy of Sciences |
nlx_144132 | SCR_005124 | 2026-02-14 02:01:03 | 0 | |||||||||
|
Digital Curation Centre Resource Report Resource Website 1+ mentions |
Digital Curation Centre (RRID:SCR_005087) | DCC | institution | The Digital Curation Centre (DCC) is a world-leading centre of expertise in digital information curation with a focus on building capacity, capability and skills for research data management across the UK''s higher education research community. The Digital Curation Centre provides expert advice and practical help to anyone in UK higher education and research wanting to store, manage, protect and share digital research data. The DCC provides access to a range of resources including our popular How-to Guides, case studies and online services. Our training programmes aim to equip researchers and data custodians with the skills they need to manage and share date effectively. We also provide consultancy and support with issues such as policy development and data management planning. | is parent organization of: DCC DIFFUSE Standards Frameworks | JISC | Wikidata: Q5275828, nlx_144098, grid.499933.d | https://ror.org/01k9d6864 | SCR_005087 | Digital Curation Center | 2026-02-14 02:01:02 | 7 | |||||||
|
California Academy of Sciences Family Science Resource Report Resource Website |
California Academy of Sciences Family Science (RRID:SCR_005241) | CAS Family Science | training resource, blog, outreach program, data or information resource, narrative resource | Family Science - Fun activities to do at home, on the web, in the Academy and more. The program serves San Francisco''s fourth and fifth grade teachers, students and their families. The Rock Program We are excited to welcome you, your students and their families to the Enhanced Museum Visits for Students Program. Generously funded by Arthur and Toni Rembe Rock, this program is open to all 4th and 5th grade classes within San Francisco County lines. Each of the following FREE features are built into the field trip program to support and enrich the museum experience for teachers, students and families: * Bus transportation - if needed * Teacher workshops that highlight exhibit themes and educational resources (required for first time participants, optional for repeat teachers) * Educational programs designed to enhance the museum visit fieldtrip for your students * A student pass entitling each student unlimited free admission through August * A one-time free family pass with a science activity book for each student valid through the end of August. | k-12, teacher, family, science, california, san francisco | has parent organization: California Academy of Sciences | Arthur and Toni Rembe Rock Fund | nlx_144244 | SCR_005241 | Family Science | 2026-02-14 02:00:53 | 0 | |||||||
|
FusionMap Resource Report Resource Website 50+ mentions |
FusionMap (RRID:SCR_005242) | FusionMap | software resource | An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI. | windows, linux, c#, fusion gene, next-generation sequencing, gene, reference indexing, read filtering, fusion alignment, reporting, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21593131 | Free, Non-commercial | biotools:fusionmap, OMICS_00316 | https://bio.tools/fusionmap | SCR_005242 | 2026-02-14 02:01:05 | 88 | ||||||
|
Traph Resource Report Resource Website 1+ mentions |
Traph (RRID:SCR_005119) | Traph | software resource | A software tool for transcript identification and quantification with RNA-Seq. The method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model. |
is listed by: OMICtools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:23734627 | Acknowledgement requested | OMICS_01295 | SCR_005119 | Transcripts in gRAPHs - Traph: A tool for transcript identification and quantification with RNA-Seq, Transcripts in gRAPHs | 2026-02-14 02:00:51 | 3 | |||||||
|
New Scientist Jobs Resource Report Resource Website |
New Scientist Jobs (RRID:SCR_005155) | New Scientist Jobs | training resource, postdoctoral program resource, job resource | At New Scientist Jobs you can search our database for hundreds of Science and Technology jobs from across the globe. Registration is free and you can upload your resume, set up email job alerts, subscribe to RSS feeds and apply for Science and Technology jobs online. Employers can post jobs. We also work in partnership with the science and academic community to help them recruit the right Science and Technology candidates for their vacancies online. | employment, career, job seeker, employer, science, technology, biochemistry, biotechnology, biostatistics, biophysics, botany, plant science, cancer research, oncology, cardiology, life science, cell biology, computational biology, developmental biology, drug development, drug discovery, ecology, epidemiology, evolutionary biology, food sciences, nutrition, forensics, genetics, genomics, gerontology/aging, immunology, informatics, marine biology, medicine, metabolism, microbiology, molecular biology, nanotechnology, neuroscience, pathology, pharmacology, physiology, proteomics, psychology, psychiatry, stem cell research, toxicology, vascular biology, veterinary medicine, virology, zoology, database, data storage repository |
is used by: NIF Data Federation is related to: Integrated Jobs |
nlx_144176 | SCR_005155 | NewScientist Jobs | 2026-02-14 02:00:50 | 0 |
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 FDI Lab - SciCrunch.org Resources search. From here you can search through a compilation of resources used by FDI Lab - SciCrunch.org and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that FDI Lab - SciCrunch.org 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 FDI Lab - SciCrunch.org then you can log in from here to get additional features in FDI Lab - SciCrunch.org 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 FDI Lab - SciCrunch.org 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.
The SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
scicrunch.org
