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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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VARIANT Resource Report Resource Website 1000+ mentions |
VARIANT (RRID:SCR_005194) | VARIANT | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line |
is listed by: OMICtools has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Science and Innovation BIO2011-27069 | PMID:22693211 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00193 | SCR_005194 | SciCrunch Registry | Variant effect, VARIant ANalysis Tool | 2026-10-24 12:45:22 | 1366 | |||||
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SNPdbe Resource Report Resource Website 1+ mentions |
SNPdbe (RRID:SCR_005190) | SNPdbe | data or information resource, data repository, database, service resource, storage service resource | A database to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. It currently covers over 155,000 protein sequences which come from more than 2,600 organisms. Overall more than one million single amino acid substitutions (SAASs) are referenced consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts. SNPdbe offers the following pieces of information (if available) on each SAAS: * Experimentally derived functional and structural impact * Predicted functional effect * Associated disease * Average heterozygosity * Experimental evidence of the nsSNP * Evolutionary conservation of wildtype and mutant amino acid * Link-outs to external databases A convenient webinterface to query SAASs on the following levels is offered: * Protein and gene identifiers and keywords * Disease keywords * Protein sequence on different sequence identity thresholds * Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence They offer the possibility to submit protein sequences along with experimentally substantiated mutations in order to predict their functional effect and inclusion into our database. | single amino acid substitution, protein variant, protein, variant, protein sequence, natural variant, mutagenesis, sequencing, mutation |
is listed by: OMICtools has parent organization: ROSTLAB |
PMID:22210871 | Free for academic use, Non-commercial, Commercial use with permission, The community can contribute to this resource | OMICS_00185 | SCR_005190 | SciCrunch Registry | SNPdbe - nsSNP database of functional effects, nsSNP database of functional effects | 2026-10-24 12:45:22 | 4 | ||||||
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CTSAconnect Resource Report Resource Website |
CTSAconnect (RRID:SCR_005225) | CTSAconnect | controlled vocabulary, data or information resource, knowledge environment, narrative resource, ontology, service resource, software resource, source code, standard specification | THIS RESOURCE IS NO LONGER IS SERVICE. Documented on December 5th, 2022. Semantic framework to integrate information about research activities, clinical activities, and scientific resources to facilitate the production and consumption of Linked Open Data about investigators, physicians, biomedical research resources, services, and clinical activities. The goal is to enable software to consume data from multiple sources and allow the broadest possible representation of researchers'''' and clinicians'''' activities and research products. Current research tracking and networking systems rely largely on publications, but clinical encounters, reagents, techniques, specimens, model organisms, etc., are equally valuable for representing expertise. CTSAConnect will provide linkage between semantic representations of a wide range of clinical and research data using controlled vocabularies mapped to the Unified Medical Language System (UMLS) as a bridge between the two subject areas. The data sources include data from Medicaid, hospital billing systems, CTSAShareCenter, and other CTSA resource data, eagle-i and VIVO. It allows institutions to leverage existing tools and data sources by making the information they contain more discoverable and easier to integrate. For instance, with the ISF, researchers can be characterized by organizational affiliations, grant and project participation, research resources that they have generated, and publications that they have (co)-authored. Clinicians can be characterized by training and credentials, by clinical research topic, and by the kinds of procedures and specialization that can be inferred from encounter data. LOD refers to data that has been given a specific Uniform Resource Identifier (URI), for the purpose of sharing and linking data and information on the Semantic Web. While a large amount of data is published as LOD, there remains a significant gap in the representation of research resources and clinical expertise. Researchers can be characterized by the organization to which they belong, the grants and research in which they have participated, the research topics and research resources (reagents, biospecimens, animal models) they have generated, as well as the publications they have (co)-authored. Clinician profiles on the other hand, can be defined by their credentials, clinical research topics, and the kinds of procedures and specialization that can be inferred from clinical encounter data. They believe that integrating and relating this diversity of information sources and platforms requires addressing the overlap between research resources and the attributes and activities of researchers and clinicians. CTSAconnect aims to promote integration and discovery of research activities, resources, and clinical expertise. To this end, they will publish their ontologies and LOD via their website, which will also illustrate repeatable methods and examples of how to extract, consume, and utilize this valuable new LOD using freely available tools like VIVO, eagle-i, and Google APIs. CTSAconnect is a collaboration between Oregon Health & Science University, Stony Brook University, Cornell University, Harvard University, University at Buffalo, and the University of Florida, and leverages the work of eagle-i (eagle-i.net), VIVO (vivoweb.org), and ShareCenter (ctsasharecenter.org). | data sharing, clinical, research, semantic framework, linked open data, collaborate |
is related to: Eagle I is related to: VIVO is related to: CTSA ShareCenter is related to: Clinical and Translational Science Awards Consortium is related to: CTSA ShareCenter has parent organization: Oregon Health and Science University; Oregon; USA has parent organization: Harvard University; Cambridge; United States |
Booz Allen Hamilton ; National Center for Advancing Translational Sciences |
THIS RESOURCE IS NO LONGER IS SERVICE | nlx_144228 | SCR_005225 | SciCrunch Registry | CTSAconnect: A Linked Open Data approach to represent clinical and research expertise activities and resources, CTSA Connect, Clinical and Translational Science Awards Connect | 2026-10-24 12:45:23 | 0 | ||||||
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qSNP Resource Report Resource Website 10+ mentions |
qSNP (RRID:SCR_005105) | qSNP | software resource | A single nucleotide variant caller optimised for identifying somatic variants in low cellularity cancer samples. |
is listed by: OMICtools has parent organization: University of Queensland; Brisbane; Australia |
Cancer | PMID:24250782 | OMICS_00089 | SCR_005105 | SciCrunch Registry | 2026-10-24 12:45:21 | 26 | ||||||||
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Damon Runyon Cancer Research Foundation Resource Report Resource Website 50+ mentions |
Damon Runyon Cancer Research Foundation (RRID:SCR_005106) | Damon Runyon Foundation | institution | The Damon Runyon Cancer Research Foundation funds early career cancer researchers who have the energy, drive and creativity to become leading innovators in their fields. We identify the best young scientists in the nation and support them through four award programs: our Fellowship, Pediatric Cancer Fellowship, Clinical Investigator and Innovation Awards. Damon Runyon awards give young scientists: * Freedom to follow their own ideas, explore new paths and take risks * A prestigious endorsement that attracts further funding, advances their careers and accelerates their research * Guaranteed financial support, sparing them hours applying for grants Since 1946, Damon Runyon has invested more than $240 million in the best young minds in the nation. Our alumni include 11 Nobel Laureates and leaders of major cancer centers across the United States. Many of our 3,300 scientists have gone on to make breakthroughs in the way we prevent, diagnose and treat many forms of cancer. The Damon Runyon Cancer Research Foundation is a registered nonprofit with 501(c)(3) status. | fellowship, grant, cancer | Crossref funder ID: 100001021, grid.453008.a, ISNI: 0000 0004 0508 2172, nlx_144117 | https://ror.org/01gd7b947 | SCR_005106 | SciCrunch Registry | 2026-10-24 12:45:21 | 67 | |||||||||
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SAMtools/BCFtools Resource Report Resource Website 1000+ 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 | SciCrunch Registry | 2026-10-24 12:45:23 | 1066 | |||||||
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MiTie Resource Report Resource Website 1+ mentions |
MiTie (RRID:SCR_005228) | MiTie | software resource | Software framework for simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples. They define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data, and show how to find the optimal solution using Mixed Integer Programming. MiTie can a) take advantage of known transcripts, b) reconstruct and quantify transcripts simultaneously in multiple samples, as well as c) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. | c++, rna-seq, transcript | is listed by: OMICtools | OMICS_01279 | SCR_005228 | SciCrunch Registry | MiTie: Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples | 2026-10-24 12:45:23 | 4 | ||||||||
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ORMAN Resource Report Resource Website 1+ mentions |
ORMAN (RRID:SCR_005188) | ORMAN | software resource | A software tool for resolving multi-mappings within an RNA-Seq SAM file. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24130305 | OMICS_01284, biotools:orman | https://bio.tools/orman | SCR_005188 | SciCrunch Registry | ORMAN : Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms | 2026-10-24 12:45:22 | 4 | ||||||
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FRCbam Resource Report Resource Website 10+ mentions |
FRCbam (RRID:SCR_005189) | software resource | Software package containing tools to process bam files in order to evaluate and analyze de novo assembly / assemblers and identify Structural Variations suspicious genomics regions. The tools have been already successfully applied in several de novo and resequencing projects. This package contains two tools: # FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers # FindTranslocations: tool to identify chromosomal rearrangements using Mate Pairs | standalone software, sam, bam | is listed by: OMICtools | PMID:23284938 | GNU General Public License, v3 | OMICS_04070 | SCR_005189 | SciCrunch Registry | 2026-10-24 12:45:22 | 11 | ||||||||
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University of KwaZulu-Natal; Durban; South Africa Resource Report Resource Website 1+ mentions |
University of KwaZulu-Natal; Durban; South Africa (RRID:SCR_005222) | UKZN | university | University with five campuses in the province of KwaZulu-Natal in South Africa. It was formed on 1 January 2004 after the merger between the University of Natal and the University of Durban-Westville. |
is parent organization of: Africa Centre Biobank is parent organization of: BioAfrica HIV Informatics in Africa is parent organization of: Africa Centre for Health and Population Studies |
nlx_51412, ISNI:0000 0001 0723 4123, Wikidata:Q727516, grid.16463.36, Crossref funder ID:501100004695 | https://ror.org/04qzfn040 | SCR_005222 | SciCrunch Registry | University of KwaZulu-Natal, University of KwaZulu Natal | 2026-10-24 12:45:23 | 4 | ||||||||
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SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | analysis service resource, data analysis service, production service resource, service resource, software resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SciCrunch Registry | SeqAnt - Sequence Annotator | 2026-10-24 12:45:22 | 2 | ||||||
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NGS-SNP Resource Report Resource Website 10+ mentions |
NGS-SNP (RRID:SCR_005182) | NGS-SNP | software resource | A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species. | annotation, snp, sequencing, transcript, genome, reference sequence, indel, annotate, reference chromosome, reference transcript, gene, command-line |
is listed by: OMICtools is related to: Ensembl has parent organization: University of Alberta; Alberta; Canada |
OMICS_00177 | SCR_005182 | SciCrunch Registry | 2026-10-24 12:45:22 | 33 | |||||||||
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Concierge Resource Report Resource Website 10+ mentions |
Concierge (RRID:SCR_002386) | Concierge | data management software, software application, software resource | A data management tool which stores, classifies and manages digital resources such as publications, experimental data, presentation files, etc, together with its metadata. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. It has a function of sharing data with open digital archives based on the XooNIps system, such as neuroinformatics platforms in operation and publicly available at J-Node (http://www.neuroinf.jp). The Concierge Project is a part of neuroinformatics research by Laboratory for Neuroinformatics in RIKEN Brain Science Institute. Concierge's primary goal is to encourage research resource sharing in neuroscience communities. A key feature of the software is its pluggable configuration. Based on the basic functions, various applications can be developed as plug-ins. It has already developed several application plug-ins specific to neuroscience research, e.g. literature manager, electronic laboratory notebook, etc. | literature manager, labnote, electronic laboratory notebook, plug-in, resource management, resource sharing |
is related to: XooNIps - Neuroinformatics Base Platform System has parent organization: RIKEN Brain Science Institute |
PMID:18974800 | Open unspecified license; Mac OS X and Windows XP versions | nif-0000-00379 | SCR_002386 | SciCrunch Registry | Concierge: Personal Database Software for Managing Digital Research Resources, Concierge Project, Concierge: Personal Database Software for Digital Research Resources, The Concierge Project: Personal Database Software for Digital Research Resources | 2026-10-24 12:44:43 | 12 | ||||||
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University of Amsterdam; Amsterdam; Netherlands Resource Report Resource Website |
University of Amsterdam; Amsterdam; Netherlands (RRID:SCR_002385) | UvA | university | Public research university in the Netherlands that offers programs in humanities, social and behavioural sciences, economics and business, science, law, medicine, and dentistry. | netherlands public university, public university, netherlands research, degree program |
is affiliated with: OpenMinTeD is parent organization of: A modular structure for scientific articles in an electronic environment is parent organization of: X-linked Adrenoleukodystrophy Database is parent organization of: T-profiler is parent organization of: 7T Structural MRI scans ATAG is parent organization of: ENVRI-KMS is parent organization of: R2 Genomics Analysis and Visualization Platform |
nlx_19684 | SCR_002385 | SciCrunch Registry | University of Amsterdam, Universiteit van Amsterdam | 2026-10-24 12:44:43 | 0 | ||||||||
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Cancer Genomics Consortium Resource Report Resource Website 1+ mentions |
Cancer Genomics Consortium (RRID:SCR_002384) | CGC | community building portal, data or information resource, organization portal, portal | Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization. | cytogenetics, molecular genetics, molecular pathology, microarray technology, cancer diagnosis, cancer research, microarry, cytogenomics, cancer cytogenomics, cancer genetics, genetics | is listed by: OMICtools | Cancer | Membership fee, Account required | OMICS_01776 | SCR_002384 | SciCrunch Registry | CCMC, Cancer Cytogenomics Microarray Consortium | 2026-10-24 12:44:46 | 6 | ||||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | data or information resource, data repository, database, service resource, storage service resource | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NCI U01 CA105417; NCRR U24 RR021760; NIAAA U01 AA014425; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIA R01 AG043930; NIDA P20 DA21131; NIGMS R01 GM123489 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | SciCrunch Registry | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-10-24 12:44:46 | 499 | |||||
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Clinical and Laboratory Standards Institute Resource Report Resource Website 100+ mentions |
Clinical and Laboratory Standards Institute (RRID:SCR_002382) | CLSI | data or information resource, knowledge environment, narrative resource, standard specification | A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world. | clinical, laboratory testing, quality, clinical laboratory testing standard, laboratory, testing | is listed by: OMICtools | Membership fee | OMICS_01777 | SCR_002382 | SciCrunch Registry | 2026-10-24 12:44:43 | 195 | ||||||||
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Neuroscience Course - Atlas Images Resource Report Resource Website 1+ mentions |
Neuroscience Course - Atlas Images (RRID:SCR_002381) | data or information resource, portal, training resource | Online educational resource for human brain and spinal cord anatomy through images. Each image is annotated with major structures and coarse dissections. | anatomy atlas, brain dissection, spinal cord dissection | has parent organization: University of Arkansas; Arkansas; USA | Public, Unauthorized use is prohibited | nif-0000-00117 | SCR_002381 | SciCrunch Registry | Neuroscience Course Atlas Images | 2026-10-24 12:44:43 | 7 | ||||||||
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MCML and CONV Resource Report Resource Website |
MCML and CONV (RRID:SCR_002419) | MCML, MCML & CONV, CONV | simulation software, software application, software resource | MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications. | optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Oregon Health and Science University; Oregon; USA |
PMID:9421660 PMID:19256707 |
Free, Available for download, Freely available | nlx_155791 | http://www.nitrc.org/projects/mcml | SCR_002419 | SciCrunch Registry | Monte Carlo for Multi-Layered media | 2026-10-24 12:44:43 | 0 | |||||
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Quick-R Resource Report Resource Website 1+ mentions |
Quick-R (RRID:SCR_002417) | Quick-R | book, data or information resource, narrative resource, training material | Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it. | r, programming language, code | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01760 | SCR_002417 | SciCrunch Registry | Quick-R - accessing the power of R | 2026-10-24 12:44:43 | 5 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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