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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Pediatric Brain Tumor Foundation Resource Report Resource Website 1+ mentions |
Pediatric Brain Tumor Foundation (RRID:SCR_004755) | PBTF | portal, data or information resource, funding resource, disease-related portal, topical portal | The Pediatric Brain Tumor Foundation (PBTF) is a nonprofit organization dedicated to eradicating childhood brain tumors and providing support to families. It is a 501(c)(3) nonprofit charitable organization that seeks to * find the cause of and cure for childhood brain tumors by supporting medical research * increase public awareness about the severity and prevalence of childhood brain tumors * aid in the early detection and treatment of childhood brain tumors * support a national database on all primary brain tumors * provide educational and emotional support for children and families affected by this life-threatening disease. As the world''s largest non-governmental source of funding for childhood brain tumor research, we''re dedicated to not only eradicating this disease, but to providing support to families. Our educational resources deliver comfort and hope to families in need of information, and our college scholarship program gives brain tumor survivors a boost for the future. Through our efforts to raise public awareness, more attention has been focused on this deadly disease. Whether addressing congressional briefings or funding international conferences, the PBTF is an unwavering advocate. Together, we''re making a difference in the lives of children with brain tumors. And with your continued help, we will cure the kids! | pediatric, brain, tumor, cancer, child, human | nlx_143893 | SCR_004755 | 2026-02-14 02:00:47 | 3 | ||||||||||
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Phymm and PhymmBL Resource Report Resource Website 10+ mentions |
Phymm and PhymmBL (RRID:SCR_004751) | Phymm, PhymmBL | software resource | Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. | metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM R01-LM006845 | PMID:19648916 PMID:21527926 |
Open-source license | OMICS_01461 | SCR_004751 | 2026-02-14 02:00:44 | 12 | ||||||
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deStruct Resource Report Resource Website 1+ mentions |
deStruct (RRID:SCR_004747) | deStruct | software resource | A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing. | structural variation, genome, genomics |
is listed by: OMICtools has parent organization: Google Code |
Tumor, Cancer | Open unspecified license | OMICS_00314 | SCR_004747 | deStruct - Bioinformatics tool for identifying structural variation in tumour genomes | 2026-02-14 02:00:59 | 7 | ||||||
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GeneDB Tbrucei Resource Report Resource Website 10+ mentions |
GeneDB Tbrucei (RRID:SCR_004786) | GeneDB_Tbrucei, GeneDB Tbrucei, GeneDB T. brucei | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries. | blast, sequence, annotation, genome |
is used by: NIF Data Federation is related to: AmiGO is related to: TriTrypDB has parent organization: GeneDB |
Wellcome Trust | PMID:16020726 | nlx_78417 | SCR_004786 | Trypanosoma brucei TREU927 homepage on GeneDB, Trypanosoma brucei TREU927 on GeneDB | 2026-02-14 02:00:45 | 17 | ||||||
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Causal Cognition Group Resource Report Resource Website 1+ mentions |
Causal Cognition Group (RRID:SCR_004780) | CCG | data or information resource, organization portal, portal, university | At the Website of the Causal Cognition Group (CCG) of the University of M��laga, you may read information about our group, its members, our research, main activities, and more. Our main interests are cognitive psychology and learning, and more recently cognitive neuroscience, physiological correlates of learning and cognitive control. This site is in constant evolution... though there are things that hardly change: Cognitio rei per causas. | computational neuroscience, cognitive neuroscience, learning, cognitive control, erp, eeg, cognitive psychology, neuroscience | has parent organization: University of Malaga; Andalusia; Spain | Junta de Andalucia ; Spanish Ministry of Science ; European Union |
nlx_143899 | SCR_004780 | Grupo Investigaci��n Aprendizaje Causal | 2026-02-14 02:00:59 | 1 | |||||||
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NCBI Probe Resource Report Resource Website 10+ mentions |
NCBI Probe (RRID:SCR_004816) | NCBI Probe | data repository, storage service resource, data or information resource, service resource, database | Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database. | reagent, probe, registry, nucleic acid, gene expression, gene mapping, gene silencing, dna data bank, nucleic acid probe, gold standard, bio.tools |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: UniSTS has parent organization: NCBI |
Public, The community can contribute to this resource | nlx_80513, r3d100010780, biotools:ncbi_dbprobe | http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe https://bio.tools/ncbi_dbprobe https://doi.org/10.17616/R3D041 |
SCR_004816 | NCBI Probe Database, Entrez Probe Database, ProbeDB, Probe Database, dbProbe | 2026-02-14 02:00:47 | 17 | ||||||
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Human Brain and Spinal Fluid Resource Center Resource Report Resource Website 1+ mentions |
Human Brain and Spinal Fluid Resource Center (RRID:SCR_004811) | HBSFRC | biomaterial supply resource, material resource, tissue bank, brain bank | A biomaterial supply resource which collects, stores, and distributes donated tissue to research scientists around the world. Collection occurs through the an anatomical donor program which accepts tissue donation from people with neurological/ psychiatric disorders. The Center also provides a continuous boost to biomedical research by providing high quality and quantity of pre- and post-mortem brains, spinal cords, cerebrospinal fluid (CSF), serum, blood cells and urine to use in investigations of neurological and psychiatric diseases. Scientists without a clinical site may use the Center''s readily available, high quality banked specimens. | neurological disorder, mental disease, tissue, pre-mortem, brain, post-mortem, spinal cord, cerebral spinal fluid, serum, blood cell, urine, blood |
is listed by: One Mind Biospecimen Bank Listing is listed by: Multiple Sclerosis Discovery Forum is related to: One Mind Biospecimen Bank Listing is related to: Multiple Sclerosis Discovery Forum has parent organization: University of California at Los Angeles; California; USA |
Neurodegenerative disease, Mental disease, Neurological disorder | NIH Blueprint for Neuroscience Research | Public, For the research community | nif-0000-00231 | http://www.loni.ucla.edu/uclabrainbank/, http://www.loni.ucla.edu/uclabrainbank/index.html | SCR_004811 | Human Brain and Spinal Fluid Resource Center (HBSFRC), The Human Brain and Spinal Fluid Resource Center (HBSFRC), UCLA Brainbank, Human Brain Spinal Fluid Resource Center, UCLA Brain Bank | 2026-02-14 02:00:47 | 6 | ||||
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Wikipedia Resource Report Resource Website 1000+ mentions |
Wikipedia (RRID:SCR_004897) | Wikipedia | narrative resource, data or information resource, wiki, database | Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Its 19 million articles (over 3.6 million in English) have been written collaboratively by volunteers around the world, and almost all of its articles can be edited by anyone with access to the site. As of July 2011, there were editions of Wikipedia in 282 languages. Wikipedia was launched in 2001 by Jimmy Wales and Larry Sanger and has become the largest and most popular general reference work on the Internet, ranking around seventh among all websites on Alexa and having 365 million readers. The name Wikipedia was coined by Larry Sanger and is a combination of wiki (a technology for creating collaborative websites, from the Hawaiian word wiki, meaning quick) and encyclopedia. Wikipedia''s departure from the expert-driven style of encyclopedia building and the large presence of unacademic content has been noted several times. Some have noted the importance of Wikipedia not only as an encyclopedic reference but also as a frequently updated news resource because of how quickly articles about recent events appear. Although the policies of Wikipedia strongly espouse verifiability and a neutral point of view, critics of Wikipedia accuse it of systemic bias and inconsistencies (including undue weight given to popular culture), and allege that it favors consensus over credentials in its editorial processes. Its reliability and accuracy are also targeted. A 2005 investigation in Nature showed that the science articles they compared came close to the level of accuracy of Encyclopedia Britannica and had a similar rate of serious errors. |
is used by: DBpedia is related to: ImpactStory is related to: WikiProject Clinical Trials is parent organization of: Comparison of web annotation systems is parent organization of: Gene Wiki is parent organization of: Cumulative Distribution Function is parent organization of: Wikibooks |
Wikimedia Foundation | nlx_86719 | SCR_004897 | 2026-02-14 02:00:48 | 1671 | |||||||||
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SEQanswers Wiki Resource Report Resource Website 1+ mentions |
SEQanswers Wiki (RRID:SCR_004810) | SEQwiki | software repository, data or information resource, wiki, software resource, narrative resource | Wiki forum providing an extensive catalogue of manually categorized analysis tools, technologies and information about service providers, maintained by the members of the SEQanswers community. * Minimum Information about a high-throughput Sequencing Experiment * Software Hub: The place to add to, edit or browse the software database on SEQwiki. * Service Providers: Browse or edit the list of NGS service facilities. * How-to Hub: Mini reviews for the most used tools broken down by common tasks. * Developers Hub: The place to discuss the development of the SEQwiki site and its associated data. See also publishing SEQ*. * Publications: Publication about SEQwiki and selected citations. | sequencing, high-throughput sequencing, service provider, next generation sequencing, next-generation genomics, genomics, data set, wiki, software |
is listed by: 3DVC is listed by: OMICtools has parent organization: SEQanswers |
PMID:22086956 | The community can contribute to this resource | OMICS_01743, nlx_143911 | SCR_004810 | 2026-02-14 02:01:00 | 1 | |||||||
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NCBI Sequence Read Archive (SRA) Resource Report Resource Website 5000+ mentions |
NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) | SRA | data repository, storage service resource, data or information resource, service resource, database | Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them. | sequence, blast, next-generation sequence, alignment, read placement, reference sequence, roche 454 gs system, illumina genome analyzer, applied biosystems solid system, helicos heliscope, complete genomics, pacific biosciences smrt, high-throughput sequencing, data analysis service, gold standard |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is listed by: OMICtools is related to: European Nucleotide Archive (ENA) is related to: RecountDB is related to: SRAdb is related to: DDBJ Sequence Read Archive is related to: Bgee: dataBase for Gene Expression Evolution is related to: NCBI BioSample is related to: DDBJ Sequence Read Archive is related to: METAGENOTE has parent organization: NCBI works with: SARS-CoV-2-Sequences works with: Signaling Pathways Project |
NLM | PMID:22009675 PMID:21062823 |
Free, Available for download, Freely available | OMICS_01031, nlx_86174, r3d100010775 | https://doi.org/10.17616/R31S69 | SCR_004891 | Sequence Read Archive, , SRA, NCBI SRA | 2026-02-14 02:01:02 | 6671 | ||||
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Anatomy Atlases Resource Report Resource Website 1+ mentions |
Anatomy Atlases (RRID:SCR_004888) | Anatomy Atlases | image collection, portal, data or information resource, book, atlas, narrative resource, topical portal | An anatomy digital health sciences library to educate patients, healthcare providers, and students in a free and anonymous manner while using current, authoritative, trustworthy health information. Anatomy Atlases addresses the continuum of anatomy education and may be of use primarily to three distinct populations. It is written for and intended primarily for use by Medical Students, Residents, Fellows, or Attending Physicians studying anatomy. Other Health Care Providers studying anatomy should find it useful. Finally, Patients (including patient''s family members or friends) may find it helpful. Anatomy Textbooks and Anatomy Atlases: * Atlas of Human Anatomy * Atlas of Human Anatomy in Cross Section * Illustrated Encyclopedia of Human Anatomic Variation * Atlas of Microscopic Anatomy - A Functional Approach: Companion to Histology and Neuroanatomy: Second Edition * Anatomy of First Aid - A Case Study Approach * Lessons From a Bone Box Lessons From a Bone Box | anatomy, atlas, first aid, histology, neuroanatomy, bone, anatomic variation | Michael P. D'Alessandro M.D. | nlx_85752 | SCR_004888 | 2026-02-14 02:01:00 | 3 | |||||||||
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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 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 | 2026-02-14 02:00:50 | 8 | ||||||||
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MycoBank Resource Report Resource Website 500+ mentions |
MycoBank (RRID:SCR_004950) | MycoBank | data repository, storage service resource, data or information resource, service resource, database | Database documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated and will also serve as Life Science Identifiers (LSIDs). Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural errors; however, no censorship whatsoever, (nomenclatural or taxonomic) will be exerted by MycoBank. Deposited names will remain -when desired- strictly confidential until after publication, and will then be accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases to realize a species bank that eventually will link all databases of life. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative. For the moment 2 search engines are available from the MycoBank website. The first one permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. The second is dedicated to bibliographic queries related to fungal name''''s publications. MycoBank users willing to deposit their data will have to register so that they willbe able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and to avoid fake entries. | yeast, aspergillus, penicillium, phaeoacremonium, russula, resupinate russulales, mycosphaerella, trichomycete, arthropod, hysteriaceae, mytilinidiaceae, mycology, nomenclature, life science identifier, bibliography, sequence alignment, polyphasic identification, image collection, FASEB list |
is listed by: SoftCite is related to: Index Fungorum |
PMID:24563843 | nlx_91803, r3d100011222 | https://doi.org/10.17616/R39D0Q | SCR_004950 | 2026-02-14 02:01:01 | 743 | |||||||
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BrainLiner Resource Report Resource Website 1+ mentions |
BrainLiner (RRID:SCR_004951) | BrainLiner | data repository, storage service resource, software library, data or information resource, service resource, software toolkit, software application, software resource, database | Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren''''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subject while he make finger-form of rock/paper/scissors). They also have a page at https://www.facebook.com/brainliner where you can contact us | brain-machine interface, brain, behavior, neurophysiology, electromyography, fmri, speech, vision, memory, neuron, eeg, electrocorticography, food tracking task, food tracking, task, meg, mutielectrode, nirs, optical imaging, pet, time-series data, neuronal spike timing, data sharing, manipulation, data set, metadata standard, neuroscience, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuroshare - Open data specifications and software for neurophysiology has parent organization: ATR; Kyoto; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26858636 | GNU General Public License, The community can contribute to this resource | nlx_91840 | SCR_004951 | BrainLiner.jp | 2026-02-14 02:00:49 | 7 | |||||
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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 | 2026-02-14 02:01:02 | 42 | ||||||||||
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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 | 2026-02-14 02:01:03 | 3 | ||||||
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Protein Data Bank Markup Language Resource Report Resource Website 1+ mentions |
Protein Data Bank Markup Language (RRID:SCR_005085) | PDBML | data or information resource, interchange format, markup language, narrative resource, standard specification | Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. | xml |
is related to: RCSB PDB Software Tools has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS |
PMID:15509603 | nlx_144096 | SCR_005085 | PDBML: Protein Data Bank Markup Language | 2026-02-14 02:01:03 | 2 | ||||||
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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 | 2026-02-14 02:01:03 | 3 | ||||||
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ArchSchema Resource Report Resource Website 1+ mentions |
ArchSchema (RRID:SCR_004947) | ArchSchema | data analysis service, analysis service resource, production service resource, source code, service resource, software application, software resource | ArchSchema is a java webstart application that generates dynamic plots of related Pfam domain architectures. The protein sequences having each architecture can be displayed on the plot and separately listed. Where there is 3D structural information in the PDB, the relevant PDB codes can be shown on the plot. Sequences can be be filtered by organism, or the output can be limited to just those protein sequences for which there is structural information in the PDB. Search by UniProt sequence id, or by Pfam domain id. Red underlines indicate the extent to which 3D structures of the domains and architectures are available in the PDB. Left-clicking on a node shows a panel containing information about the constituent domains, the protein sequences having the given architecture, and any sequences that have whole or partial structures in the PDB. You can display protein sequence (or, alternatively, the protein structures) associated with each architecture. You can download ArchSchema to run locally from your own machine. Note, however, you only download the code and not the data. Thus you will need to be connected to the Internet whenever you perform a search from within ArchSchema. The search initiates a call to the EBI which returns the data to ArchSchema for graphing. | gold standard |
is related to: PDBsum has parent organization: European Bioinformatics Institute |
PMID:20299327 | nlx_91580 | SCR_004947 | ArchSchema - graphs of related Pfam domain architectures | 2026-02-14 02:00:49 | 1 | |||||||
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European Genome phenome Archive Resource Report Resource Website 500+ mentions |
European Genome phenome Archive (RRID:SCR_004944) | EGA | data repository, storage service resource, web service, data set, data or information resource, service resource, data access protocol, software resource | Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication. | phenomenon, trait, sequence, genotype, experiment, case-control, population, family study, snp, cnv, phenotype, genomic, gold standard, bio.tools |
is used by: Blueprint Epigenome is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:34791407 | Restricted | BioTools:ega, biotools:ega, r3d100011242, OMICS_01028, nlx_91316 | https://ega-archive.org/ https://bio.tools/ega https://bio.tools/ega https://doi.org/10.17616/R3W619 |
SCR_004944 | , The European Genome-phenome Archive, The European Genome-phenome Archive (EGA), EGA | 2026-02-14 02:01:01 | 605 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
