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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
QuRe Resource Report Resource Website 1+ mentions |
QuRe (RRID:SCR_005209) | QuRe | software resource | A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions. | next-generation sequencing, virus, long read, reconstruction |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00230 | SCR_005209 | qure - software for viral quasispecies reconstruction from next-gen seq. data | 2026-02-14 02:00:52 | 6 | ||||||||
|
VirusFinder Resource Report Resource Website 10+ mentions |
VirusFinder (RRID:SCR_005205) | VirusFinder | software resource | Software tool for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. Specifically, it detects virus infection, co-infection with multiple viruses, virus integration sites in host genomes, as well as mutations in the virus genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing. | next-generation sequencing, virus, integration site, genome, mutation, virus genome, contig, paired-end, single-end, whole genome sequencing, whole transcriptome sequencing, rna-seq, targeted sequencing, whole exome sequencing, ultra-deep amplicon sequencing |
is listed by: OMICtools has parent organization: Vanderbilt University; Tennessee; USA |
Viral infection | PMID:23717618 | OMICS_00226 | SCR_005205 | 2026-02-14 02:01:05 | 16 | |||||||
|
RNA-eXpress Resource Report Resource Website 1+ mentions |
RNA-eXpress (RRID:SCR_005167) | RNA-eXpress | software resource | Software designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Monash University; Melbourne; Australia |
PMID:23396121 | Acknowledgement requested, Non-Profit | biotools:rna-express, OMICS_01285 | https://bio.tools/rna-express | SCR_005167 | 2026-02-14 02:01:04 | 5 | ||||||
|
Kavli Foundation Resource Report Resource Website 1+ mentions |
Kavli Foundation (RRID:SCR_005113) | Kavli Foundation | institution | The Kavli Foundation, based in Oxnard, California, is dedicated to advancing science for the benefit of humanity, promoting public understanding of scientific research, and supporting scientists and their work. The Foundation''s mission is implemented through an international program of research institutes, professorships, symposia and other initiatives in the fields of astrophysics, nanoscience, neuroscience and theoretical physics. The Foundation is also a founding partner of the Kavli Prizes, which recognize scientists for their seminal advances in astrophysics, nanoscience and neuroscience. To date, The Kavli Foundation has made grants to establish Kavli Institutes on the campuses of the University of California Santa Barbara, Stanford University, the California Institute of Technology, the University of Chicago, Columbia University, Yale University, Cornell University, the University of California San Diego, Delft University of Technology in the Netherlands, the Massachusetts Institute of Technology, Peking University, the Chinese Academy of Sciences, Harvard University, the University of Cambridge and the Norwegian University of Science and Technology. In addition to the Kavli Institutes, six Kavli professorships have been established: two at the University of California Santa Barbara, one at University of California Los Angeles, one at the University of California Irvine, one at Columbia University, and one at the California Institute of Technology. The Kavli Futures Symposia a series of high quality scientific symposia on topics of emerging importance in the fields of astrophysics, nanoscience and neuroscience. The Frontiers of Science symposia bring together some of the very best young scientists across many disciplines to share and discuss exciting advances and opportunities in their fields. Videos and feature pieces have been created for teachers and students. This includes video interviews with acclaimed researchers Eric Kandel, M.D. and Edvard and May-Britt Moser, a video introduction and panel discussion on neuroscience, feature stories, written science overview, institute profiles and other materials. The Kavli Foundation is a private foundation qualified under IRC Section 501 (c) (3). | award, prize, neuroscience, astrophysics, nanoscience, theoretical physics, brain | ISNI: 0000 0004 0405 1139, grid.453241.5, Wikidata: Q27788485, Crossref funder ID: 100001201, nlx_144120 | https://ror.org/00kztt736 | SCR_005113 | The Kavli Foundation | 2026-02-14 02:01:02 | 9 | ||||||||
|
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 | ||||||||
|
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 | |||||||||
|
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 | |||||||
|
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 | |||||||
|
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 | ||||||||
|
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 | |||||||||
|
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 | |||||||
|
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 | ||||||||
|
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 | ||||||
|
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 | ||||||||
|
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 | ||||||||
|
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 | |||||||||
|
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 | ||||||||
|
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 | ||||||||||
|
ISRNA Resource Report Resource Website 1+ mentions |
ISRNA (RRID:SCR_009565) | ISRNA | software resource | An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | PMID:24300438 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00360 | SCR_009565 | Integrative Short Reads NAvigator | 2026-02-14 02:01:41 | 3 | |||||||
|
NordicNeuroLab Resource Report Resource Website 50+ mentions |
NordicNeuroLab (RRID:SCR_009632) | NNL | commercial organization | From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike. | analyze, ascii, dicom, diffusion mr fiber tracking, experiment control, eye tracking, fiber tracking, haemodynamic response, hardware, microsoft, magnetic resonance, nifti, perfusion, physiological recording, scanner, stimulus presentation, temporal curve fitting, temporal transformation, tractography, windows, windows vista, windows xp, fmri, post-processing, visualization, bold, diffusion, dti, perfusion, dce, audio stimulation, visual stimulation, eye tracking, patient response, clinical, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial | nlx_155905 | http://www.nitrc.org/projects/nnl | SCR_009632 | 2026-02-14 02:01:53 | 53 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
