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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Benaroya Research Institute Resource Report Resource Website 1+ mentions |
Benaroya Research Institute (RRID:SCR_001272) | BRI | institution | Non-profit organization based out of Seattle, Washington that conducts medical research on autoimmune disease. | research institute, nonprofit, medical, autoimmune disease |
is parent organization of: Immune Tolerance Network (ITN) is parent organization of: Benaroya Research Institute: Neurological Diseases is parent organization of: Benaroya Research Institute Cell and Tissue Analysis Group Core Facility is parent organization of: Benaroya Research Institute Human Immunophenotyping Core Facility is parent organization of: Benaroya Research Institute Genomics Core Facility is parent organization of: Benaroya Research Institute BRI Biorepository Core Facility |
, Wikidata Q4886865, nlx_152837, ISNI 0000 0004 0444 3749 | https://ror.org/04j9rp686 | SCR_001272 | SciCrunch Registry | Benaroya Research Institute at Virginia Mason, Benaroya | 2026-10-24 12:44:28 | 1 | |||||||
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mBPCR Resource Report Resource Website |
mBPCR (RRID:SCR_001273) | mBPCR | software resource | Software package that estimates the DNA copy number profile to detect regions with copy number changes. | copy number variation, microarray, snp, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02065 | SCR_001273 | SciCrunch Registry | mBPCR - Bayesian Piecewise Constant Regression for DNA copy number estimation | 2026-10-24 12:44:32 | 0 | |||||||
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CGHregions Resource Report Resource Website 1+ mentions |
CGHregions (RRID:SCR_001278) | CGHregions | software resource | Software package for dimension Reduction for Array CGH Data with Minimal Information Loss. | copy number variation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19455235 | Free, Available for download, Freely available | OMICS_02058 | SCR_001278 | SciCrunch Registry | CGHregions - Dimension Reduction for Array CGH Data with Minimal Information Loss | 2026-10-24 12:44:32 | 4 | ||||||
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CGHbase Resource Report Resource Website 1+ mentions |
CGHbase (RRID:SCR_001279) | CGHbase | data analysis software, data processing software, software application, software resource | Software package that contains functions and classes that are needed by arrayCGH packages. | copy number variation, infrastructure, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02057 | SCR_001279 | SciCrunch Registry | CGHbase: Base functions and classes for arrayCGH data analysis | 2026-10-24 12:44:28 | 1 | |||||||
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quantsmooth Resource Report Resource Website 1+ mentions |
quantsmooth (RRID:SCR_001271) | quantsmooth | software resource | Software package for quantile smoothing and genomic visualization of array data. | copy number variation, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:15572474 | Free, Available for download, Freely available | OMICS_02067, BioTools:quantsmooth, biotools:quantsmooth | https://bio.tools/quantsmooth, https://bio.tools/quantsmooth, https://bio.tools/quantsmooth | SCR_001271 | SciCrunch Registry | 2026-10-24 12:44:30 | 1 | ||||||
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SNPchip Resource Report Resource Website 10+ mentions |
SNPchip (RRID:SCR_001269) | SNPchip | software resource | Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality. | dna copy number, snp, genetic variability, visualization, high throughput, snp chip, microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:17204461 | Free, Available for download, Freely available | OMICS_02069, biotools:snpchip | https://bio.tools/snpchip | SCR_001269 | SciCrunch Registry | 2026-10-24 12:44:32 | 14 | ||||||
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Simpleaffy Resource Report Resource Website 50+ mentions |
Simpleaffy (RRID:SCR_001302) | Simpleaffy | data analysis software, data processing software, software application, software resource | Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures. | affymetrix, annotation, data import, differential expression, microarray, one channel, preprocessing, quality control, report writing, transcription, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16076888 | GNU General Public License, v2 or newer | OMICS_02034 | SCR_001302 | SciCrunch Registry | Simpleaffy - Very simple high level analysis of Affymetrix data | 2026-10-24 12:44:32 | 85 | ||||||
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ADMIXTURE Resource Report Resource Website 1000+ mentions |
ADMIXTURE (RRID:SCR_001263) | ADMIXTURE | software resource | A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ancestry, macos x, linux, admixture, allele, genome, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
PMID:19648217 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:admixture, OMICS_02077 | http://www.genetics.ucla.edu/software/admixture/ | SCR_001263 | SciCrunch Registry | ADMIXTURE: fast ancestry estimation | 2026-10-24 12:44:28 | 2699 | |||||
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frappe Resource Report Resource Website 50+ mentions |
frappe (RRID:SCR_001264) | frappe | software resource | Software using a f frequentist approach for estimating individual ancestry proportion. | ancestry, admixture, genome, allele |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:15712363 | Free, Available for download, Freely available | OMICS_02076 | SCR_001264 | SciCrunch Registry | 2026-10-24 12:44:32 | 56 | |||||||
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ipPCA Resource Report Resource Website 1+ mentions |
ipPCA (RRID:SCR_001262) | ipPCA, i2pPCA | software resource | Software implementing a population structure analysis algorithm which assigns individuals to subpopulations and infers the total number of subpopulations present. Additional functions have been included that result in improved population assignment accuracy. # Universal genotype data encoding scheme which allows the population analysis of all types of genetic markers; Single Nucleotide Polymorphism (SNP), Short Tandem Repeat (STR) and RFLP. # New termination criterion called ?EigenDev? which is more robust to population sampling, thus provides the better estimation of number of assigned subpopulations (K) and higher accuracy for the analysis of large complex population datasets. | principal component analysis, population, genetic marker, single nucleotide polymorphism, short tandem repeat, rflp | is listed by: OMICtools | PMID:21699684 PMID:19930644 |
Free, Available for download, Freely available | OMICS_02078 | http://www4a.biotec.or.th/GI/tools/ippca | SCR_001262 | SciCrunch Registry | i2pPCA, Iterative pruning Principal Component Analysis | 2026-10-24 12:44:30 | 1 | |||||
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VegaMC Resource Report Resource Website 1+ mentions |
VegaMC (RRID:SCR_001267) | VegaMC | software resource | Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported. | copy number variation, acgh, chromosomal imbalance |
is listed by: OMICtools is related to: PennCNV has parent organization: Bioconductor |
Cancer | PMID:22815357 | Free, Available for download, Freely available | OMICS_02071 | SCR_001267 | SciCrunch Registry | VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer | 2026-10-24 12:44:30 | 1 | |||||
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VanillaICE Resource Report Resource Website 1+ mentions |
VanillaICE (RRID:SCR_001268) | VanillaICE | software resource | Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. | statistics, dna copy number, snp, genetic variability, visualization, high throughput, snp chip, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:19609370 | GNU General Public License, v2 or newer | OMICS_02070 | http://www.biostat.jhsph.edu/~rscharpf/software/index.html | SCR_001268 | SciCrunch Registry | vanilla-ice | 2026-10-24 12:44:28 | 3 | |||||
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Mutascope Resource Report Resource Website 1+ mentions |
Mutascope (RRID:SCR_001265) | Mutascope | data analysis software, data processing software, software application, software resource | Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. | high throughput sequencing, pcr amplicon, pcr, mutation, amplicon, sequencing, somatic variant |
is listed by: OMICtools has parent organization: SourceForge |
Tumor, Normal | PMID:23712659 | Free, Public | OMICS_02074 | SCR_001265 | SciCrunch Registry | Mutascope - Analysis software designed for PCR-amplicon sequencing data | 2026-10-24 12:44:28 | 4 | |||||
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GemTools Resource Report Resource Website 10+ mentions |
GemTools (RRID:SCR_001259) | GemTools | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R. | genetic, ancestry, single nucleotide polymorphism, r |
is listed by: OMICtools has parent organization: University of Pittsburgh; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02079 | SCR_001259 | SciCrunch Registry | GemTools - A fast and efficient approach to estimating genetic ancestry | 2026-10-24 12:44:28 | 45 | |||||||
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SCAN.UPC Resource Report Resource Website 10+ mentions |
SCAN.UPC (RRID:SCR_001334) | SCAN.UPC | software resource | A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A | microarray, one channel, preprocessing, rna-seq, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02006 | SCR_001334 | SciCrunch Registry | Single-channel array normalization (SCAN) and Universal exPression Codes (UPC), Single-channel array normalization and Universal exPression Codes | 2026-10-24 12:44:31 | 11 | |||||||
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EEGbase Resource Report Resource Website 1+ mentions |
EEGbase (RRID:SCR_001452) | data or information resource, data repository, database, service resource, storage service resource | EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework. | eeg, erp, experiments, data storage and management, EEG/ERP data, EEG/ERP experiments, |
uses: NIX uses: Open metadata mark up language is used by: NIF Data Federation has parent organization: University of West Bohemia; Pilsen; Czech Republic |
Ministry of Education Czech Science Foundation | Free, Freely Available | nif-0000-08190 | http://eegdatabase.kiv.zcu.cz/ | SCR_001452 | SciCrunch Registry | 2026-10-24 12:44:34 | 7 | |||||||
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betr Resource Report Resource Website 10+ mentions |
betr (RRID:SCR_001332) | betr | software resource | Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data. | differentially expression, gene, microarray, time-course |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20003283 | Free, Available for download, Freely available | OMICS_01997 | http://www.bioconductor.org/packages/release/bioc/html/betr.html | SCR_001332 | SciCrunch Registry | Bayesian Estimation of Temporal Regulation | 2026-10-24 12:44:33 | 17 | |||||
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Wake Forest University School of Medicine: Department of Neurology Resource Report Resource Website |
Wake Forest University School of Medicine: Department of Neurology (RRID:SCR_001453) | data or information resource, department portal, organization portal, portal, university | Department at the Wake Forest University's School of Medicine that hosts physicians who specialize in neurological topics such as neuromuscular disease, epilepsy, pediatric neurology, strokes, neuropsychology, neurosonology, and neurorehabilitaiton. | neurology, medicine, wake forest, stroke, neuropsychology, physicain | Free, Freely Available | nif-0000-10549 | http://www1.wfubmc.edu/neurology/ | SCR_001453 | SciCrunch Registry | WFUBMC Neurology | 2026-10-24 12:44:33 | 0 | ||||||||
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Roche Resource Report Resource Website 500+ mentions |
Roche (RRID:SCR_001326) | commercial organization | A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics. | pharmaceutical, diagnostic, drug, medicine, commercial |
is affiliated with: European Federation of Pharmaceutical Industries and Associations is related to: EU-AIMS is related to: eTRIKS is related to: OncoTrack is related to: GetReal is related to: IMIDIA is related to: Kinetics for Drug Discovery is related to: NEWMEDS is related to: PharmaCog is related to: PREDECT is related to: EMIF is parent organization of: EU-AIMS is parent organization of: Genentech is parent organization of: Roche Diagnostics is parent organization of: Roche: cobas�� e 601 |
ISNI: 0000 0004 1759 0967, grid.486917.5, nlx_152451, Wikidata: Q41568432 | https://ror.org/02hv5e369 | SCR_001326 | SciCrunch Registry | Hoffmann-La Roche AG, Hoffmann-La Roche, Roche Holding AG, F. Hoffmann-La Roche, F. Hoffmann-La Roche Ltd | 2026-10-24 12:44:31 | 544 | ||||||||
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gprege Resource Report Resource Website 1+ mentions |
gprege (RRID:SCR_001324) | gprege | software resource | Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007). | differential expression, microarray, preprocessing, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21599902 | Free, Available for download, Freely available | OMICS_02011, biotools:gprege | http://www.bioconductor.org/packages/release/bioc/html/gprege.html | SCR_001324 | SciCrunch Registry | Gaussian Process Ranking and Estimation of Gene Expression time-series | 2026-10-24 12:44:33 | 1 |
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