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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GenoSet Resource Report Resource Website |
GenoSet (RRID:SCR_001275) | GenoSet | data analysis software, data processing software, software application, software resource | Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. | copy number variation, data representation, infrastructure, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License, v2 | OMICS_02063 | SCR_001275 | SciCrunch Registry | genoset - Provides classes similar to ExpressionSet for copy number analysis | 2026-09-26 02:12:57 | 0 | |||||||
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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 | 2026-09-26 02:12:57 | 1 | |||||||
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CISCRP- The Center for Information and Study on Clinical Research Participation Resource Report Resource Website |
CISCRP- The Center for Information and Study on Clinical Research Participation (RRID:SCR_001152) | data or information resource, portal, topical portal | CISCRP is a resource for information on participation in, understanding of, and resources for clinical research participants and scientists. The mission of the Center is to educate, inform and empower patients, the public, medical and research professionals, the media and policymakers about clinical research participation and what it means to be an active participant in the clinical research process, promote greater awareness and understanding of clinical research participation and the role that it plays in public health, facilitate more effective collaboration among all members of the clinical research enterprise, and provide resources for the research community to better understand the study volunteer. To that end, the Center has developed a broad national awareness and education initiative in order to better inform the public at large about clinical study information. Furthermore, on its website, the Center offers program and event information related to clinical trials, an information center with facts, figures, informational resources, and FAQs for both patients and researchers, and a mailing list of clinical trial information. :The Center also maintains its own search engine website, : :searchclinicaltrials.org : : :, for those looking for further clinical trial information. The Center for Information and Study on Clinical Research Participation is located in Dedham, MA. :NIF thanks the : :Parkinson's Disease Foundation : : :for their referral of this resource to us. | clinical research, clinical study | nif-0000-11642 | SCR_001152 | SciCrunch Registry | CISCRP | 2026-09-26 02:12:55 | 0 | ||||||||||
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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 | 2026-09-26 02:12:57 | 0 | |||||||
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massiR Resource Report Resource Website |
massiR (RRID:SCR_001157) | software resource | Software that predicts the sex of samples in gene expression microarray datasets. | standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24659105 | Free, Available for download, Freely available | biotools:massir, OMICS_03638 | https://bio.tools/massir | SCR_001157 | SciCrunch Registry | massiR: MicroArray Sample Sex Identifier, MicroArray Sample Sex Identifier | 2026-09-26 02:12:55 | 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 | 2026-09-26 02:12:57 | 4 | ||||||
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CenterWatch Resource Report Resource Website 1+ mentions |
CenterWatch (RRID:SCR_001158) | data or information resource, portal, topical portal | CenterWatch is an online resource for news, directories, analysis, and proprietary market research for clinical research professionals and patients. For patients, CenterWatch is committed to providing information on clinical trials, specific drugs, as well as other essential health and educational resources. On this website, patients can search clinical trials, receive e-mail notifications about specific clinical trials, review results from completed clinical trials, search drug information, learn about volunteering for a clinical trial, read an overview of the clinical trials process and find other health and educational resources. For researchers, CenterWatch offers a wide range of tools and resources to improve patient and investigator recruitment, remain current with industry trends and business practices, and strengthen organizational procedures. CenterWatch also offers information on grant opportunities, and a variety of educational books and publications. Researchers can provide the public with information about their clinical trials by using the Clinical Trials Listing Serviceprovided through CenterWatch, or look up more specific information on medicines and equipment using Drug and Device Pipeline News. Overall, the mission of CenterWatch is to be the leading source of news, directories, analysis, and proprietary market research for clinical research professionals and patients. It is located in Boston, MA. :NIF thanks the :Parkinson's Disease Foundation : :for their referral of this resource to us. | drug information, drug study, clinical research, clinical study, clinical trial, medicine, patient, health, medical | nif-0000-11641 | SCR_001158 | SciCrunch Registry | CenterWatch | 2026-09-26 02:12:55 | 9 | ||||||||||
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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 | 2026-09-26 02:12:57 | 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 | 2026-09-26 02:12:57 | 1 | ||||||
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Intramodal Registration Software Resource Report Resource Website |
Intramodal Registration Software (RRID:SCR_001148) | data analysis software, data processing software, software application, software resource | Software that implements a set of C routines for robust, high-quality registration of two volumes, aligning according to a least-squares criterion which is well-suited to intramodal registration tasks. Programming skills are required to attach the ANSI-C routine to whichever system users have. It is available on Unix, Macintosh, and PC. | intramodal registration, unix, pc, macintosh, programming, c | has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland | Free, Available for download, Freely available | nif-0000-00318 | SCR_001148 | SciCrunch Registry | 2026-09-26 02:12:55 | 0 | |||||||||
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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 | 2026-09-26 02:12:57 | 14 | ||||||
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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 | 2026-09-26 02:12:57 | 2699 | |||||
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NeuroMouse Database Resource Report Resource Website |
NeuroMouse Database (RRID:SCR_001143) | NeuroMouse | atlas, data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17, 2023.Toolbook(tm) based, interactive graphical database which provides structural, molecular, and genetic information on the adult murine nervous system; and its relevance to human neurobiology. This resource is primarily designed as a platform for users to interact, each sharing knowledge on their own area of expertise, which is compiled to a master database. This hypertext atlas presently comprises more than 1000 pages and is designed to provide a flexible integrated resource for the description and discussion of all forms mammalian neurologic data. Version 4.0 of the NeuroMouse program extends the program's basic framework to include a number of areas in modern molecular neurobiology. This system provides an integrated resource for the characterization and description of mammalian neurological data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas. Neuromouse has been integrated into our strain-specific three dimensional MRI and surgical atlases of the murine CNS. Database contents: Neural Atlas: - Rotational representation of the murine brain. - Neural structures: visual and alphabetic point and click index of neural structures, pathways and systems. - Brain atlas:photographic serial sections in the coronal, sagittal, and horizontal planes (average plate distance - 300 um). Physical brain distances are also provided as are meta-index grids to allow rapid movement between different planes and regions. # Catalog of primary and immortalized neural cells indexed to relevant neural structures. Molecular Atlas: - Index of neurotransmitters: Acetylcholine, GABA, Glutamate, Aspartate, Glycine, Dopamine, Norepinephrine, Epinephrine, Serotonin (synthesis, distribution, degradation, molecular modules, receptors, subunits, agonists, antagonists, gene structure, localization, physical properties and transgenics are indicated for each item). - Index of neurotrophins / neurokines: NGF, BDNF, NT-3, NT-4/5, CNTF, LIF, Onostain M, IL-6, GDNF, FGF's, S100b (ligand, receptors, expression pattern, physical properties, homologous factors, transgenics/knockouts, chromosomal location, effects of agent, and effects of factors on agent are indicated for each item). - Index of additional neural agents: Bcl-2, TNF/Fas, TGF-beta, P53/Rb, PDGF, EGF family (ligand, receptor, expression patterns, physical properties, homologous factors, transgenics/ knockouts, chromosomal location, effects of agent, effects of factors on agent are indicated for each item). - Molecular biology: Molecular biology of important neural genes with integrated l links, plus selected neural topics (ex. programmed cell death, inducible gene systems, protein motifs, neural gene elements, and selected signal transduction pathways). Genetics Atlas: - Lesion paradigms: Index of common neuronal structural and chemical lesion paradigms. - Selected procedures: description of common neurosurgical, cell tracing, culturing and laboratory procedures. - Neurologic syndromes: Index of important human neurologic syndromes and appropriate animals models. - Neural mutant database: Index and description of naturally occurring and genetically modified murine neurologic mutations; including pages on double knockout animals. Interactive maps of each murine chromosome and human syntenic maps. | epinephrine, gaba, acetylcholine, agonist, antagonist, aspartate, dopamine, glutamate, glycine, human, molecular biology, murine chromosome, mutant, neural, neural factor, neurokine, neurological, neurotransmitter, n eurotrophin, norepinephrine, serotonin, molecular neuroanatomy resource, nervous system, adult, murine | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11000 | SCR_001143 | SciCrunch Registry | 2026-09-26 02:12:55 | 0 | |||||||||
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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 | 2026-09-26 02:12:57 | 56 | |||||||
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Phoenix Pharmaceuticals Resource Report Resource Website 1000+ mentions |
Phoenix Pharmaceuticals (RRID:SCR_001141) | commercial organization | Commercial antibody supplier that specializes in peptide-related products for research in obesity, cardiovascular disease, and diabetes. | antibody, peptide, obesity, cardiovascular, diabetes, commercial, biomaterial supply resource | nlx_152429 | SCR_001141 | SciCrunch Registry | Phoenix Pharmaceuticals Inc. | 2026-09-26 02:12:55 | 1136 | ||||||||||
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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 | 2026-09-26 02:12:57 | 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 | 2026-09-26 02:12:57 | 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 | 2026-09-26 02:12:57 | 3 | |||||
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Translational Research Laboratory Resource Report Resource Website |
Translational Research Laboratory (RRID:SCR_001023) | data or information resource, portal, topical portal | Cancer research laboratory at the Peter MacCallum Cancer Centre which investigates biomarkers identification, compounds for activity as anti-cancer drugs, and small molecule targeted therapies. | translational research, cancer, therapeutics, biomarker, small molecule |
is listed by: ScienceExchange is related to: Peter Mac Translational Research Laboratory |
SciEx_10351 | https://www.scienceexchange.com/labs/translational-research-laboratory | http://www.scienceexchange.com/facilities/peter-maccallum-cancer-centre | SCR_001023 | SciCrunch Registry | Peter MacCallum Cancer Centre - Cancer Therapeutics Program | 2026-09-26 02:12:54 | 0 | |||||||
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Reaper - Demultiplexing trimming and filtering sequencing data Resource Report Resource Website 1+ mentions |
Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) | Reaper | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data. | c, alignment, sequence, demultiplex, trim, filter, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:reaper, OMICS_02157 | https://bio.tools/reaper | SCR_001144 | SciCrunch Registry | 2026-09-26 02:12:55 | 1 |
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