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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
University of Iowa; Iowa; USA Resource Report Resource Website 1+ mentions |
University of Iowa; Iowa; USA (RRID:SCR_005011) | UI | university | Public research university in Iowa City, Iowa. Founded in 1847, it is the oldest and the second-largest university in the state. |
is affiliated with: Big Ten Cancer Research Consortium is related to: Clinical and Translational Science Awards Consortium is parent organization of: I/OWA is parent organization of: Hardin MD is parent organization of: Non-Rigid Image Registration Evaluation Project is parent organization of: Brief Psychiatric Rating Scale is parent organization of: University of Iowa Carver College of Medicine; Iowa; USA is parent organization of: Hereditary Hearing Loss Homepage is parent organization of: BRAINSTools is parent organization of: Bayesian Output Analysis Program is parent organization of: Brain Research: Analysis of Images, Networks and Systems is parent organization of: BRAINSDemonWarp is parent organization of: GTRACT is parent organization of: University of Iowa Labs and Facilities is parent organization of: NeuroNEXT is parent organization of: GazeReader is parent organization of: Human Thalamus in 3D Stereotactic Coordinates is parent organization of: University of Iowa Institute of Human Genetics Genomics Division Core Facility is parent organization of: University of Iowa Roy J Carver Center for Imaging Core Facility is parent organization of: University of Iowa Roy J Carver Center for Genomics Core Facility hosts: DSHB |
nlx_52860, grid.214572.7, ISNI:0000 0004 1936 8294, Wikidata:Q45133494, Crossref funder ID:100008893 | https://ror.org/036jqmy94 | SCR_005011 | University of Iowa | 2026-08-01 12:02:52 | 8 | ||||||||
|
Pythia Resource Report Resource Website 10+ mentions |
Pythia (RRID:SCR_004952) | software resource | Pythia is an open source thermodynamically oriented primer design python module. Pythia can be used in two ways. 1. Executable binaries only: under windows with cygwin and python 2.5 (built with mingw, that comes with the cygwin release). These executables allow the user to index DNA files for primer specificity search, design one primer pair per region, and tile regions with PCR amplicons. 2. A python module: under windows with cygwin, python2.5, numpy, swig, and mingw, or under linux with python2.4 or later, numpy, and swig (everything but numpy should be pre-installed on a normal linux system). The module gets you everything that the binaries get you, in a more pythonic framework. This package also includes modules for computing DNA binding and folding energies using the partition function approach with publicly available thermodynamic data. Usage documentation is in the downloads. | has parent organization: SourceForge | PMID:19528077 | nlx_91969 | SCR_004952 | 2026-08-01 12:02:47 | 42 | ||||||||||
|
SLIQ Resource Report Resource Website 1+ mentions |
SLIQ (RRID:SCR_005003) | SLIQ | software resource | Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph. | python, scaffolding, contig position, contig orientation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:23057825 | biotools:sliq, OMICS_00048 | https://bio.tools/sliq | SCR_005003 | Simple linear inequalities, SLiQ: Simple linear inequalities based Mate-Pair reads filtering and scaffolding | 2026-08-01 12:02:51 | 3 | ||||||
|
cortex var Resource Report Resource Website 1+ mentions |
cortex var (RRID:SCR_005081) | cortex_var | software resource | A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM | genome assembly, variation analysis, sequence, variation, genotype variant, haploid, diploid, snp, indel, inversion, variant, haplotype, de novo assembly, genotyping, variant-calling, population analysis, population assembly |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:22231483 | GNU General Public License, v3, Acknowledgement requested | OMICS_00056 | SCR_005081 | cortex_var - for variant and population assembly | 2026-08-01 12:02:54 | 3 | ||||||
|
Applied Biosystems Resource Report Resource Website 10000+ mentions |
Applied Biosystems (RRID:SCR_005039) | commercial organization | An Antibody supplier | is parent organization of: Ambion Inc. | nlx_152278 | SCR_005039 | 2026-08-01 12:02:48 | 32510 | |||||||||||
|
SOPRA Resource Report Resource Website 10+ mentions |
SOPRA (RRID:SCR_005035) | SOPRA | software resource | Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:20576136 | Acknowledgement requested | biotools:sopra, OMICS_00049 | https://bio.tools/sopra | SCR_005035 | SOPRA - Statistical Optimization of Paired Read Assembly, Statistical Optimization of Paired Read Assembly | 2026-08-01 12:02:48 | 20 | |||||
|
Bioworld Technology Resource Report Resource Website 1+ mentions |
Bioworld Technology (RRID:SCR_005036) | commercial organization | An Antibody supplier | nlx_152317 | SCR_005036 | 2026-08-01 12:02:52 | 1 | ||||||||||||
|
SSPACE Resource Report Resource Website 100+ mentions |
SSPACE (RRID:SCR_005056) | SSPACE | software resource | A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. | scaffolding, contig, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21149342 DOI:10.1093/bioinformatics/btq683 |
GNU General Public License, Registration required | biotools:sspace, OMICS_00050 | https://bio.tools/sspace, https://sources.debian.org/src/sspace/ | SCR_005056 | 2026-08-01 12:02:53 | 426 | ||||||
|
HPC-CLUST Resource Report Resource Website 1+ mentions |
HPC-CLUST (RRID:SCR_005052) | HPC-CLUST | software resource | A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead. | c++, mpi |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:24215029 | OMICS_01446 | SCR_005052 | 2026-08-01 12:02:48 | 5 | ||||||||
|
University of Manchester; Manchester; United Kingdom Resource Report Resource Website 1+ mentions |
University of Manchester; Manchester; United Kingdom (RRID:SCR_004996) | university | Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment. |
is affiliated with: OpenMinTeD is related to: NEWMEDS is related to: ORBITO is related to: Open PHACTS is related to: EMIF is parent organization of: Smart Dictionary Lookup is parent organization of: mlgt is parent organization of: Utopia Docs is parent organization of: Kidney and Urinary Pathway Knowledge Base is parent organization of: PUMA is parent organization of: DOSY Toolbox is parent organization of: RightField is parent organization of: SEEK is parent organization of: miRBase is parent organization of: PRINTS is parent organization of: CHEM21 is parent organization of: Taverna is parent organization of: SysMO-DB is parent organization of: MethodBox is parent organization of: OWL API is parent organization of: X:MAP is parent organization of: Mimas is parent organization of: National Centre for Text Mining is parent organization of: Chemistry Using Text Annotations is parent organization of: TerMine is parent organization of: Acromine Disambiguator is parent organization of: Census Dissemination Unit is parent organization of: Open Regulatory Annotation Database is parent organization of: ADAPT: A Database of Affymetrix Probesets and Transcripts is parent organization of: brat rapid annotation tool is parent organization of: UK DNA Banking Network is parent organization of: AcroMine is parent organization of: BioIE: Extracting Informative Sentences From the Biomedical Literature is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: myExperiment is parent organization of: Software Ontology is parent organization of: bioNerDS is parent organization of: MorphoJ is parent organization of: University of Manchester Bioinformatics Core Facility is parent organization of: miRBase is parent organization of: Simple Assignment of Spots to Surfaces is parent organization of: AMBER parameter database is parent organization of: University of Manchester Electron Microscopy Core Facility is parent organization of: University of Manchester Mass Spectrometry and Separations Core Facility is parent organization of: University of Manchester Advanced Manufacturing Platform Core Facility is parent organization of: University of Manchester Surface Characterisation Core Facility is parent organization of: University of Manchester Biochemical and Biophysical Sciences Technology Platform Core Facility is parent organization of: University of Manchester Corrosion and Materials for Demanding Environments Core Facility is parent organization of: University of Manchester Magnetic Resonance and Related Technology Platform Core Facility is parent organization of: University of Manchester X-ray Diffraction Platform Core Facility is parent organization of: University of Manchester Services and Equipment Core Facility is parent organization of: University of Manchester Design, Fabrication and Testing Core Facility is parent organization of: University of Manchester National X-ray Computed Tomography Core Facility is parent organization of: University of Manchester Advanced Metal Development Core Facility is parent organization of: University of Manchester BioAutomation and Biofoundry Core Facility is parent organization of: University of Manchester Biomolecular NMR Core Facility has organization facet: MANC-RISK-SCREEN |
nlx_74265, Wikidata:Q230899, grid.5379.8, ISNI:121662407, Crossref funder ID:501100000770 | https://ror.org/027m9bs27 | SCR_004996 | University of Manchester | 2026-08-01 12:02:44 | 7 | |||||||||
|
Bio X Cell Resource Report Resource Website 1000+ mentions |
Bio X Cell (RRID:SCR_004997) | commercial organization | Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services. | commercial, antibody, reagent, biomedical, research, new hampshire, | SCR_019248, nlx_152318 | SCR_004997 | 2026-08-01 12:02:47 | 4386 | |||||||||||
|
ESPRIT-Tree Resource Report Resource Website 1+ mentions |
ESPRIT-Tree (RRID:SCR_005045) | ESPRIT-Tree | software resource | Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time. | clustering, 16s rrna, pyrosequence |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:21596775 | OMICS_01445 | SCR_005045 | ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time | 2026-08-01 12:02:53 | 9 | |||||||
|
MBCluster.Seq Resource Report Resource Website 1+ mentions |
MBCluster.Seq (RRID:SCR_005079) | MBCluster.Seq | software resource | Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24191069 | GNU General Public License, >/=v3 | OMICS_01417, biotools:mbcluster.seq | https://bio.tools/mbcluster.seq | SCR_005079 | MBCluster.Seq: Model-Based Clustering for RNA-seq Data | 2026-08-01 12:02:48 | 1 | |||||
|
AGORA Resource Report Resource Website 50+ mentions |
AGORA (RRID:SCR_005070) | AGORA | software resource | An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences. | genome assembly, genome, reconstruction | is listed by: OMICtools | PMID:22856673 | OMICS_00039 | SCR_005070 | Assembly Guided by Optical Restriction Alignment | 2026-08-01 12:02:45 | 99 | |||||||
|
GRASS Resource Report Resource Website 50+ mentions |
GRASS (RRID:SCR_005071) | GRASS | software resource | A generic algorithm for scaffolding next-generation sequencing assemblies. | next-generation sequencing, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22492642 | GNU General Public License, v3 | biotools:GRASS, OMICS_00043 | https://bio.tools/GRASS | SCR_005071 | GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies, GeneRic ASembly Scaffolder | 2026-08-01 12:02:48 | 89 | |||||
|
MapAl Resource Report Resource Website 1+ mentions |
MapAl (RRID:SCR_004938) | MapAl | software resource | A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably. | rna?seq |
is listed by: OMICtools has parent organization: BOKU University; Vienna; Austria |
PMID:22485116 | GNU General Public License | OMICS_01261 | SCR_004938 | 2026-08-01 12:02:43 | 1 | |||||||
|
Open University; Milton Keynes; United Kingdom Resource Report Resource Website 1+ mentions |
Open University; Milton Keynes; United Kingdom (RRID:SCR_004931) | OU | university | Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world. |
is affiliated with: OpenMinTeD is parent organization of: Scholarly Ontologies Project is parent organization of: Cohere is parent organization of: Rexplore |
Wikidata:Q2413375, nlx_19814, grid.10837.3d, ISNI:96069301, Crossref funder ID:100008509 | https://ror.org/05mzfcs16 | SCR_004931 | Open University, The Open University | 2026-08-01 12:02:43 | 3 | ||||||||
|
University of Iowa Carver College of Medicine; Iowa; USA Resource Report Resource Website 1+ mentions |
University of Iowa Carver College of Medicine; Iowa; USA (RRID:SCR_005064) | UI Carver College of Medicine | university | Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa. |
has parent organization: University of Iowa; Iowa; USA is parent organization of: MADS+ - discovery of differential splicing events from Affymetrix exon junction array data is parent organization of: University of Iowa College of Medicine Department of Pharmacology is parent organization of: University of Iowa Magnetic Resonance Research Facility is parent organization of: University of Iowa Center for Gene Therapy Vectore Core is parent organization of: University of Iowa Center for Gene Therapy Clinical Core is parent organization of: University of Iowa Center for Gene Therapy Animal Model Core is parent organization of: University of Iowa Center for Gene Therapy is parent organization of: University of Iowa Center for Gene Therapy Comparative Pathology Core is parent organization of: University of Iowa Center for Gene Therapy Cell Tissue Core |
nlx_68753 | SCR_005064 | University of Iowa Carver College of Medicine, Roy J. and Lucille A. Carver College of Medicine | 2026-08-01 12:02:53 | 1 | |||||||||
|
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 | 2026-08-01 12:02:49 | 2 | |||||||||
|
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 | 2026-08-01 12:02:49 | 32 |
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.
