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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CCAT Resource Report Resource Website 50+ mentions |
CCAT (RRID:SCR_001843) | CCAT | software resource | THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:20371496 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00428, biotools:ccat | https://bio.tools/ccat | SCR_001843 | Control based ChIP-Seq Analysis Tools | 2026-02-14 02:00:09 | 76 | |||||
|
Alt Event Finder Resource Report Resource Website |
Alt Event Finder (RRID:SCR_001846) | Alt Event Finder | software resource | Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only. | alternative splicing, rna-seq, alternative splicing event, transcript, annotation, splicing regulation |
is listed by: OMICtools is related to: Cufflinks is related to: Scripture has parent organization: Indiana University; Indiana; USA |
PMID:23281921 | Free, Freely available | OMICS_01941 | SCR_001846 | Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data | 2026-02-14 02:00:20 | 0 | ||||||
|
ExpressionPlot Resource Report Resource Website 1+ mentions |
ExpressionPlot (RRID:SCR_001904) | expressionplot | software resource | Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. | analysis, rna-seq, microarray, gene expression, affymetrix, prototype | is listed by: OMICtools | PMID:21797991 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01939 | SCR_001904 | 2026-02-14 02:00:14 | 9 | |||||||
|
S-MART Resource Report Resource Website 10+ mentions |
S-MART (RRID:SCR_001908) | S-MART | software resource | Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries. | high throughput sequencing, rna-seq, chip-seq, python, linux, ms windows, mac, short-read, selection, visualization, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21998740 | Free, Available for download, Freely available | OMICS_01937, biotools:mapperanalyzer, biotools:s-mart | https://bio.tools/s-mart https://bio.tools/mapperanalyzer |
SCR_001908 | 2026-02-14 02:00:11 | 23 | ||||||
|
Korea Advanced Institute of Science and Technology; Daejeon; South Korea Resource Report Resource Website 1+ mentions |
Korea Advanced Institute of Science and Technology; Daejeon; South Korea (RRID:SCR_001902) | KAIST | institution | Institute dedicated to research in science and technology in South Korea modeled after a research university. | south korea, research, science, technology |
is parent organization of: NIRS-SPM is parent organization of: FiGS |
Available to the research community | grid.37172.30, ISNI: 0000 0001 2292 0500, Crossref funder ID: 501100007107, Wikidata: Q39949, nlx_155859 | https://ror.org/05apxxy63 | http://www.kaist.edu/english/ | SCR_001902 | Korea Advanced Institute of Science and Technology | 2026-02-14 02:00:14 | 1 | |||||
|
THetA Resource Report Resource Website 100+ mentions |
THetA (RRID:SCR_001860) | software resource | An algorithm that estimates the tumor purity and clonal / subclonal copy number aberrations directly from high-throughput DNA sequencing data. | standalone software |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
PMID:23895164 | Free, Available for download, Freely available | OMICS_03562 | http://compbio.cs.brown.edu/projects/theta/ | SCR_001860 | THetA: Tumor Heterogeneity Analysis, Tumor Heterogeneity Analysis, Tumor Heterogeneity Analysis (THetA) | 2026-02-14 02:00:13 | 204 | ||||||
|
University of Alberta; Alberta; Canada Resource Report Resource Website 1+ mentions |
University of Alberta; Alberta; Canada (RRID:SCR_001853) | university | Public research university in Edmonton, Alberta, Canada that offers degree programs in a variety of fields including business, arts, education, engineering, nursing, and medicine. | public, research, university, alberta, canada |
is related to: Alberta Diabetes Institute IsletCore database is parent organization of: T3DB is parent organization of: DrugBank is parent organization of: Arthur Prochazka Laboratory, University of Alberta is parent organization of: Proteome Analyst Specialized Subcellular Localization Server is parent organization of: Canadian Biosample Repository is parent organization of: Blood Borne Pathogens Laboratory is parent organization of: Small Molecule Pathway Database is parent organization of: NGS-SNP is parent organization of: PHAge Search Tool is parent organization of: PolySearch is parent organization of: YMDB - Yeast Metabolome Database is parent organization of: BacMap: Bacterial Genome Atlas is parent organization of: HMDB is parent organization of: Proteome Analyst is parent organization of: Proteome Analyst PA-GOSUB is parent organization of: CGView is parent organization of: UAlberta Cell Imaging Centre is parent organization of: UAlberta Institute for Biomolecular Design is parent organization of: UAlberta Mass Spectrometry Facility - Department of Chemistry is parent organization of: University of Alberta Labs and Facilities is parent organization of: CCDB - The CyberCell Database is parent organization of: VKCDB - Voltage-gated K Channel Database is parent organization of: Human Metabolome Database is parent organization of: Proteome Analyst is parent organization of: Neuromembrane Simulator is parent organization of: MetaboAnalyst is parent organization of: MetaboAnalyst is parent organization of: Alberta University Diabetes Institute IsletCore Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Transgenic Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Lipidomics Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Flow Cytometry Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Cell Imaging Centre Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Autoclave Repair Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Workshop Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry High Content Analysis Core Facility is parent organization of: University of Alberta Precision Human Health Laboratory Core Facility provides: Heatmapper |
Free, Freely available | nlx_10148 | SCR_001853 | University of Alberta | 2026-02-14 02:00:13 | 7 | ||||||||
|
SamSPECTRAL Resource Report Resource Website 1+ mentions |
SamSPECTRAL (RRID:SCR_001858) | software resource | Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry, stem cell, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Cancer, HIV | PMID:20667133 | Free, Available for download, Freely available | OMICS_05638, biotools:samspectral | https://bio.tools/samspectral | SCR_001858 | SamSPECTRAL - Identifies cell population in flow cytometry data | 2026-02-14 02:00:13 | 4 | |||||
|
San Diego Supercomputer Center Resource Report Resource Website 1+ mentions |
San Diego Supercomputer Center (RRID:SCR_001856) | SDSC | institution | Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing. SDSC is considered a leader in data-intensive computing, providing resources, services and expertise to the national research community including industry and academia. The mission of SDSC is to extend the reach of scientific accomplishments by providing tools such as high-performance hardware technologies, integrative software technologies, and deep interdisciplinary expertise to these communities. From 1997 to 2004, SDSC extended its leadership in computational science and engineering to form the National Partnership for Advanced Computational Infrastructure (NPACI), teaming with approximately 40 university partners around the country. Today, SDSC is an Organized Research Unit of the University of California, San Diego with a staff of talented scientists, software developers, and support personnel. A broad community of scientists, engineers, students, commercial partners, museums, and other facilities work with SDSC to develop cyberinfrastructure-enabled applications to help manage their extreme data needs. Projects run the gamut from creating astrophysics visualization for the American Museum of Natural History, to supporting more than 20,000 users per day to the Protein Data Bank, to performing large-scale, award-winning simulations of the origin of the universe or how a major earthquake would affect densely populated areas such as southern California. Along with these data cyberinfrastructure tools, SDSC also offers users full-time support including code optimization, training, 24-hour help desk services, portal development and a variety of other services. As one of the NSF's first national supercomputer centers, SDSC served as the data-intensive site lead in the agency's TeraGrid program, a multiyear effort to build and deploy the world's first large-scale infrastructure for open scientific research. SDSC currently provides advanced user support and expertise for XSEDE (Extreme Science and Engineering Discovery Environment) the five-year NSF-funded program that succeeded TeraGrid in mid-2011. | engineering, bioinformatics, computing, geoinformatics, hardware, industry, science, software, technology, computational science, supercomputing, cyberinfrastructure |
has parent organization: University of California at San Diego; California; USA is parent organization of: Scaffold builder is parent organization of: OpenTopography is parent organization of: chronopolis is parent organization of: XSEDE - Extreme Science and Engineering Discovery Environment is parent organization of: Family Pairwise Search - Protein Family Classification is parent organization of: Neuroscience Gateway is parent organization of: Magnetics Information Consortium |
NSF | Free, Freely available | nif-0000-10418, Wikidata: Q3947008, grid.419957.7 | https://ror.org/04mg3nk07 | SCR_001856 | 2026-02-14 02:00:09 | 5 | ||||||
|
National Society of Genetic Counselors Resource Report Resource Website 10+ mentions |
National Society of Genetic Counselors (RRID:SCR_001803) | NSGC | institution | Professional society of genetic counselors that promotes networking, continuing education opportunities, advocacy, and discussion of relevant issues in the field of genetics. | genetics, counselor, advocacy, professional society, professional network | Free | Crossref funder ID: 100010237, grid.429579.4, nif-0000-10367, ISNI: 0000 0001 2179 5189 | https://ror.org/02ja4sy98 | SCR_001803 | National Society of Genetic Counselors (NSGC) | 2026-02-14 02:00:08 | 16 | |||||||
|
RchyOptimyx Resource Report Resource Website 1+ mentions |
RchyOptimyx (RRID:SCR_001889) | software resource | Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response). | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23044634 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05637 | SCR_001889 | RchyOptimyx - Optimyzed Cellular Hierarchies for Flow Cytometry, RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry | 2026-02-14 02:00:14 | 3 | |||||||
|
CQN Resource Report Resource Website 1+ mentions |
CQN (RRID:SCR_001786) | CQN | software resource | A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. | rna-seq, differential expression, preprocessing, 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:22285995 | Free, Available for download, Freely available | OMICS_01949, biotools:cqn | https://bio.tools/cqn | SCR_001786 | Conditional Quantile Normalization | 2026-02-14 02:00:11 | 6 | |||||
|
PoissonSeq Resource Report Resource Website 10+ mentions |
PoissonSeq (RRID:SCR_001784) | PoissonSeq | software resource | Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data. | normalization, testing, false discovery rate, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
PMID:22003245 | Free, Available for download, Freely available | OMICS_01950 | http://cran.r-project.org/web/packages/PoissonSeq/index.html | SCR_001784 | PoissonSeq: Significance analysis of sequencing data based on a Poisson log linear model | 2026-02-14 02:00:11 | 33 | |||||
|
Kindai University; Osaka; Japan Resource Report Resource Website |
Kindai University; Osaka; Japan (RRID:SCR_001814) | university | Private non-sectarian and coeducational university based in Higashiosaka, Osaka, Japan. | private, university, osaka, japan | is parent organization of: Kindai University School of Medicine; Osaka; Japan | Free | ISNI:0000 0004 1936 9967, nlx_149308, grid.258622.9, Wikidata:Q912329 | https://ror.org/05kt9ap64 | SCR_001814 | Kinki University | 2026-02-14 02:00:12 | 0 | |||||||
|
Pennsylvania State Hershey College of Medicine; Pennsylvania; USA Resource Report Resource Website |
Pennsylvania State Hershey College of Medicine; Pennsylvania; USA (RRID:SCR_002019) | university | Public, land-grant research university in Pennsylvania, USA. The College of Medicine offers professional degree programs in medicine. | medicine, public, research, university |
has parent organization: Pennsylvania State University is parent organization of: Pennsylvania State University College of Medicine Neuroscience is parent organization of: Penn State College of Medicine Genome Sciences Core Facility is parent organization of: Penn State Hershey College of Medicine Clinical Research Biospecimen Core Facility is parent organization of: Penn State Hershey College of Medicine MRI Core Facility is parent organization of: Penn State Hershey College of Medicine Zebrafish Functional Genomics Core Facility is parent organization of: Penn State Hershey College of Medicine Transmission Electron Microscopy Core Facility is parent organization of: Penn State Hershey College of Medicine Light Microscopy Imaging Core Facility is parent organization of: Pennsylvania State University Hershey College of Medicine Custom Antibody Core Facility is parent organization of: Penn State College of Medicine High Performance Computing Core Facility is parent organization of: Penn State Hershey College of Medicine Comparative Medicine Imaging Core Facility is parent organization of: Penn State College of Medicine Biomolecular NMR Core Facility is parent organization of: Penn State Hershey College of Medicine Atomic Force Microscopy Core Facility is parent organization of: Penn State College of Medicine Pulmonary Immunology and Physiology Core Facility is parent organization of: Penn State Hershey College of Medicine Institutional Biorepository Core Facility |
nlx_82737 | http://med.psu.edu/web/college/home | SCR_002019 | Penn State Hershey College of Medicine; Pennsylvania; USA, Pennsylvania State Hershey College of Medicine, Penn State Hershey College of Medicine | 2026-02-14 02:00:17 | 0 | ||||||||
|
SNPper Resource Report Resource Website 10+ mentions |
SNPper (RRID:SCR_001963) | SNPper | software resource | Retrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions. | single-nucleotide polymorphism, gene, chromosome |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:12490454 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01926 | SCR_001963 | 2026-02-14 02:00:21 | 49 | |||||||
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National Center for PTSD Resource Report Resource Website 10+ mentions |
National Center for PTSD (RRID:SCR_001967) | NCPTSD | institution | We are the center of excellence for research and education on the prevention, understanding, and treatment of PTSD. Our Center has seven divisions across the country. Although we provide no direct clinical care, our purpose is to improve the well-being and understanding of American Veterans. We conduct cutting edge research and apply resultant findings to: Advance the Science and Promote Understanding of Traumatic Stress. The National Center has emerged as the world's leading research and educational center of excellence on PTSD. Its vision is to be the foremost leader in information on PTSD and trauma; information generated internally through its extensive research program, and information synthesized from published scientific research and collective clinical experience that is efficiently disseminated to the field. The Center is organized to facilitate rapid translation of science into practice, assuring that the latest research findings inform clinical care; and translation of practice into science, assuring that questions raised by clinical challenges are addressed using rigorous experimental protocols. By drawing on the specific expertise vested at each separate division (e.g., behavioral, neuroscientific, etc.), the National Center provides a unique infrastructure within which to implement multidisciplinary initiatives regarding the etiology, pathophysiology, diagnosis and treatment of PTSD. | post-traumatic stress disorder, stress, trauma, treatment, stress-related disorder, clinical care, human, traumatic stress disorder, one mind ptsd | has parent organization: U.S. Department of Veterans Affairs | US Department of Veterans Affairs | nif-0000-10538, grid.497281.1, ISNI: 0000 0004 0374 606X | https://ror.org/01dbbht76 | http://www.ncptsd.va.gov/ | SCR_001967 | National Center for Posttraumatic Stress Disorder, VA National Center for PTSD | 2026-02-14 02:00:12 | 11 | |||||
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Neurofed Resource Report Resource Website |
Neurofed (RRID:SCR_002011) | Neurofed | people resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The NeuroFed resource is a listing of neuroscience research funding contacts in the Federal government. It is an informal compendium (PDF) of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units of the federal government. An electronic (PDF) version of the most recent update of this list is available on the Society for Neuroscience website at: http://www.sfn.org/index.aspx?pagename=professionalDevelopment_training. The list is updated annually by NIH personnel. |
is used by: NIF Data Federation has parent organization: National Institutes of Health |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10988 | SCR_002011 | 2026-02-14 02:00:16 | 0 | |||||||||
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Parkinson Society Canada Resource Report Resource Website 1+ mentions |
Parkinson Society Canada (RRID:SCR_002014) | nonprofit organization | A not-for-profit, volunteer based charity whose purpose is to find a cure for Parkinson's disease through research, advocacy, education and support services. Parkinson Society Canadas leads initiatives that include: raising funds for research through national events; funding research, movement disorder clinics, and outreach programs across Canada; staffing a national Information and Referral Centre; developing educational and information materials; providing up to date detailed information about Parkinson's disease; and providing support for regional partners to better meet the needs of people living with Parkinson's services. Researchers can apply for various funding awards and fellowships by following the funding process outlined by Parkinson Society Canada. | parkinson's disease, parkinson's disease online community, parkinson's disease organizations, parkinson's disease patient care, parkinson's disease therapy, parkinson's disease treatment center | Parkinson's Disease | Public, Funding is available to researchers in the form of awards and fellowships | grid.453461.1, Crossref funder ID: 501100000263, nif-0000-11672 | https://ror.org/04amfk357 | SCR_002014 | 2026-02-14 02:00:13 | 3 | ||||||||
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Model 1025 MR-compatible Small Animal Monitoring and Gating System Resource Report Resource Website 1+ mentions |
Model 1025 MR-compatible Small Animal Monitoring and Gating System (RRID:SCR_002090) | Model 1025 Monitoring & Gating System | instrument resource | Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2. | hardware, instrument, equipment, physiology, monitoring, gating, mr environment, respiration, temperature, blood pressure, oxygen saturation, end-tidal co2, magnetic resonance, electrocardiogram, magnetic resonance imaging, software resource | Free, Freely available | SciRes_000157 | https://wikihost.uib.no/mriwiki/images/4/4c/SAInstruments_1025.pdf | http://www.i4sa.com/web_app/main/defaultProduct.aspx?ID=82&PT=3 | SCR_002090 | Model 1025 Monitoring and Gating System, MR-Compatible Model 1025 Monitoring and Gating System, Small Animal Monitoring and Gating System | 2026-02-14 02:00:22 | 3 |
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