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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NRF Contacts Resource Report Resource Website |
NRF Contacts (RRID:SCR_001473) | NRF Contacts | data or information resource, data set, people resource | This resource provides a list of federal program officials in the neurosciences. An informal compendium of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units. | director, military, neurodegenerative disease, program officer, 2008, neuroscience | has parent organization: Society for Neuroscience | NIH ; NIMH ; U.S. Department of Health and Human Services |
nif-0000-09488 | http://www.sfn.org/nrfcontacts | SCR_001473 | SciCrunch Registry | Neuroscience Research Funding Contacts in the Federal Government, Neuroscience Research Funding Contacts | 2026-09-26 02:13:00 | 0 | ||||||
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Human Brain Connectivity Database Resource Report Resource Website |
Human Brain Connectivity Database (RRID:SCR_001594) | Human Brain Connectivity Database | bibliography, data or information resource, data set | Preliminary database of neuroanatomical connectivity reports specifically for the human brain, which have been manually curated. It includes details (based on manual literature curation) of tract tracing or related connectivity studies conducted in human brain tissue. This database and user interface will be expanded and improved in the near future. | neuroanatomy, brain, tract tracing, connectivity | has parent organization: Brain Architecture Project | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153841 | SCR_001594 | SciCrunch Registry | 2026-09-26 02:13:01 | 0 | ||||||||
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MACAT Resource Report Resource Website |
MACAT (RRID:SCR_001350) | MACAT | software resource | Software library that contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. | differential expression, microarray, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:15572464 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01989, biotools:macat | https://bio.tools/macat | SCR_001350 | SciCrunch Registry | MicroArray Chromosome Analysis Tool | 2026-09-26 02:12:58 | 0 | |||||
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Waxholm Space Resource Report Resource Website 10+ mentions |
Waxholm Space (RRID:SCR_001592) | WHS, WSA, WSS | atlas, data or information resource, narrative resource, standard specification, waxholm atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files. | mouse WHS atlas, neuroanatomy, mapping, atlas, digital, brain, reference, registration, neuroanatomical, data, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Waxholm Space is related to: Duke University; North Carolina; USA is related to: PMOD Software is related to: ITK-SNAP has parent organization: International Neuroinformatics Coordinating Facility has parent organization: University of Oslo; Oslo; Norway works with: MeshView works with: VisuAlign |
PMID:20600960 PMID:21304938 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_009594, nlx_153838, nlx_155839 | http://software.incf.org/software/waxholm-space/home, http://www.nitrc.org/projects/incf_waxholm-sp | SCR_001592 | SciCrunch Registry | Waxholm Space Atlas, Waxholm Space, Waxholm Standard Space, Mouse WHS atlas | 2026-09-26 02:13:01 | 16 | |||||
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Neurologychannel Resource Report Resource Website 1+ mentions |
Neurologychannel (RRID:SCR_001597) | data or information resource, portal, topical portal | A topical portal which provides information about conditions that affect the nervous system (brain, spinal cord, nerves, and muscles), such as stroke (brain attack), Alzheimer's disease, and back pain. It is a physician developed and monitored source of neurology information for consumers. Additionally, it contains comprehensive condition and treatment information, as well as interactive tools. | alzheimer's disease, back pain, brain, developed, disease, information, monitored, muscle, nerve, nervous system, neurology, physician, spinal cord, stroke | Alzheimer's Disease | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10380 | SCR_001597 | SciCrunch Registry | neurologychannel | 2026-09-26 02:13:01 | 1 | ||||||||
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BLASTN Resource Report Resource Website 10000+ mentions |
BLASTN (RRID:SCR_001598) | BLASTn | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast. | nucleotide, alignment, compare, sequence, genome, blast, transcript, dna sequence |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI works with: Seek and Blastn works with: RMBlast |
PMID:17666756 PMID:18567917 |
Free, Freely available | nlx_153932, OMICS_00990 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001598 | SciCrunch Registry | NCBI BLASTN, Nucleotide Blast, Standard Nucleotide BLAST | 2026-09-26 02:13:01 | 21160 | |||||
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Bilkent University; Ankara; Turkey Resource Report Resource Website |
Bilkent University; Ankara; Turkey (RRID:SCR_001474) | university | Private university located in Ankara, Turkey that offers undergraduate and graduate programs in fields that include economics, art and architecture, languages, and neuroscience. | private, education, university, ankara, economics, art, architecture, languages, neuroscience | Free, Freely Available | nlx_95218 | SCR_001474 | SciCrunch Registry | Bilkent University | 2026-09-26 02:13:00 | 0 | |||||||||
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nnNorm Resource Report Resource Website |
nnNorm (RRID:SCR_001354) | nnNorm | software resource | Software package that allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01985 | SCR_001354 | SciCrunch Registry | nnNorm - Spatial and intensity based normalization of cDNA microarray data based on robust neural nets | 2026-09-26 02:12:59 | 0 | |||||||
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Type 1 Diabetes Resource Resource Report Resource Website 1+ mentions |
Type 1 Diabetes Resource (RRID:SCR_001475) | T1DR | biomaterial supply resource, material resource, organism supplier | International repository for importation, curation, genotypic and phenotypic validation, cryopreservation, and distribution of mouse stocks of value to the type 1 diabetes scientific community holding over 250 genetically modified or congenic mouse stocks that are being used to dissect genetic and biologic features of T1D. They provide extensive genotypic and phenotypic quality control and genetic stabilization for these strains, as well as incidence studies when available. An added value of T1DR stocks is their ability to propel advances in related areas of science, including research in non-T1D autoimmunity and infectious diseases. The staff provides information and technical assistance regarding selection and use of existing T1DR models, and will provide limited support for development of new models considered to be of high-value for the T1D community. The resource includes strains generated at the Jackson Laboratory as well as strains donated by external scientists. Investigators are highly encouraged to donate a strain to ensure its preservation and availability to other researchers. | genotype, phenotype, animal model |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) has parent organization: Jackson Laboratory |
Type 1 diabetes, Diabetes | NIDDK UC4DK097610 | Free, Freely Available | nlx_152730 | SCR_001475 | SciCrunch Registry | 2026-09-26 02:13:00 | 1 | ||||||
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maCorrPlot Resource Report Resource Website 1+ mentions |
maCorrPlot (RRID:SCR_001348) | maCorrPlot | software resource | Software that graphically displays correlation in microarray data that is due to insufficient normalization. | microarray, preprocessing, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15799785 | Free, Available for download, Freely available | OMICS_01991 | SCR_001348 | SciCrunch Registry | maCorrPlot - Visualize artificial correlation in microarray data | 2026-09-26 02:12:58 | 2 | ||||||
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The Cromwell Workshop Resource Report Resource Website |
The Cromwell Workshop (RRID:SCR_001588) | TCW | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. Statistical and biomedical informatics software studio that develops neuroscience applications and brain computer interface games. They are dedicated to the integration of medical research, neuroscience, time series analysis, computer programming, statistics, sensor technologies, graphics design, artificial intelligence and entertainment to build gaming systems for neuroscientific research and intelligent tutoring in the classroom and lab. The current focus of The Cromwell Workshop/Neuronal Architects is on theoretical neuroscience and experimental modeling of psychological and neural processes that involve attention, emotion, motivation and executive functions that are impaired by neurological diseases. The outcome of this work is to use these results in the design of multiple genre brain computer interface gaming systems that can be used in both clinical and at home settings. If you would like to explore any collaborative opportunities to use their software or enhance your existing statistical products with their .NET, Java, R and Matlab code bases, let them know. | statistical software, web design, medical research, neuroscience, time series analysis, computer programming, statistics, sensor technology, graphics design, artificial intelligence, entertainment, gaming system, modeling, psychological process, neural process, attention, emotion, motivation, executive function, neurological disease, brain computer interface, .net, java, r, matlab, computational neuroscience, time series, gaming |
is parent organization of: Neural Maestro is parent organization of: Neural Cipher is parent organization of: iBIOFind is parent organization of: eNeoTutor is parent organization of: ModelMaker |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153830 | SCR_001588 | SciCrunch Registry | Cromwell Workshop | 2026-09-26 02:13:01 | 0 | |||||||
|
lapmix Resource Report Resource Website |
lapmix (RRID:SCR_001347) | lapmix | software resource | Software to identify differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. | differential expression, microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:lapmix, OMICS_01992 | https://bio.tools/lapmix | SCR_001347 | SciCrunch Registry | Laplace Mixture Model in Microarray Experiments | 2026-09-26 02:12:58 | 0 | ||||||
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rMAT Resource Report Resource Website 10+ mentions |
rMAT (RRID:SCR_001583) | data analysis software, data processing software, software application, software resource, source code | Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program. | chip-seq, normalize data, tiling array, mat, r |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20089513 | Free, Available for download, Freely available | OMICS_00810 | http://www.rglab.org | SCR_001583 | SciCrunch Registry | 2026-09-26 02:13:01 | 16 | |||||||
|
FARMS Resource Report Resource Website 10+ mentions |
FARMS (RRID:SCR_001344) | FARMS | software resource | Software using a model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. | oligonucleotide array, probe, affymetrix genechip, r, unix, windows, microarray, summarization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johannes Kepler University of Linz; Linz; Austria |
PMID:16473874 | Free, Freely Available | OMICS_01995, biotools:farms | https://bio.tools/farms | SCR_001344 | SciCrunch Registry | Factor Analysis for Robust Microarray Summarization | 2026-09-26 02:12:58 | 28 | |||||
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Collaborative Islet Transplant Registry Resource Report Resource Website 1+ mentions |
Collaborative Islet Transplant Registry (RRID:SCR_001466) | CITR | data or information resource, data repository, database, narrative resource, report, resource, service resource, storage service resource | Collect, analyze, and communicate on comprehensive and current data on all islet/beta cell transplants in human recipients performed in North America, as well as some European and Australian centers to expedite progress and promote safety in islet/beta cell transplantation. This site serves as a repository for general information concerning protocols, clinical transplantation sites, publications, and other information of interest to the general community. Annual Reports are available. Islet/beta cell transplantation is a complex procedure with many factors contributing to the outcome. Compiling and analyzing data from all transplant centers in the US, Canada, as well as some European and Australian centers will accelerate the identification of both critical risk factors and key determinants of success and thereby guide transplant centers in developing and refining islet/beta cell transplant protocols. The inclusion of the term collaborative in the name of the Registry emphasizes the importance of collaboration in fulfilling the CITR mission and goals. Close collaboration with the transplant centers will ensure that relevant questions are addressed, that data submitted are accurate and complete, and that the needs of the transplant community are served. Information on how to participate as a CITR Transplant Center and to receive a transplant center application is available through the website. Progress in islet transplantation depends entirely on complete, high-quality medical data, including the information patients consented to report to the Collaborative Islet Transplant Registry. To make it as easy as possible to provide updated information about patient's health, an on-line questionnaire is available or patients can mail it to their transplant center. This information is very important in the continuing search for a cure for Type 1 diabetes. | transplant center, transplant, islet, beta cell, clinical, islet transplantation, beta cell transplantation, outcome, metadata standard, adverse event report, diabetes, data element, bibliography, questionnaire, protocol, risk factor, case report form, allograft, pancreatectomy, autograft, islet processing | is listed by: NIDDK Information Network (dkNET) | Type 1 diabetes, Diabetes | NIDDK N01-DK6-2868; NIDDK N01-DK1-2472 |
PMID:15387102 | Free, Freely Available | nlx_152693 | SCR_001466 | SciCrunch Registry | 2026-09-26 02:13:00 | 9 | |||||
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iBIOFind Resource Report Resource Website |
iBIOFind (RRID:SCR_001587) | iBIOFind | data or information resource, database, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles. | workflow, model, prediction, research trend, rare disease, resource discovery, biomedicine, genomic, neural network, visualization, reporting, search engine, genetic, neural, clinical translation science award, biomedical resource, funding, gene, protein, neuron, collaborator, publication, trend, grant, funding opportunity, report |
is related to: ModelMaker is related to: Neural Maestro is related to: eNeoTutor is related to: Cytoscape is related to: Biomedical Resource Ontology is related to: PubMed has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153829 | SCR_001587 | SciCrunch Registry | 2026-09-26 02:13:01 | 0 | ||||||||
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OCplus Resource Report Resource Website 1+ mentions |
OCplus (RRID:SCR_001342) | OCplus | software resource | Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). | differential expression, microarray, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16368770 | Free, Available for download, Freely available | OMICS_01999 | SCR_001342 | SciCrunch Registry | Ocplus - Operating characteristics plus sample size and local fdr for microarray experiments | 2026-09-26 02:12:58 | 1 | ||||||
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bridge Resource Report Resource Website 100+ mentions |
bridge (RRID:SCR_001343) | bridge | software resource | Software package to test for differentially expressed genes with microarray data. It can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. The model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. | cdna microarray, affymetrix chip, differential expression, microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:16542223 | Free, Available for download, Freely available | OMICS_01996, biotools:bridge | http://www.bioconductor.org/packages/release/bioc/html/bridge.html | SCR_001343 | SciCrunch Registry | Bayesian Robust Inference for Differential Gene Expression | 2026-09-26 02:12:58 | 157 | |||||
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CALIB Resource Report Resource Website 100+ mentions |
CALIB (RRID:SCR_001338) | CALIB | software resource | Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17485432 | Free, Available for download, Freely available | OMICS_02003 | http://www.bioconductor.org/packages/release/bioc/html/CALIB.html | SCR_001338 | SciCrunch Registry | 2026-09-26 02:12:58 | 141 | ||||||
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vsn Resource Report Resource Website 1+ mentions |
vsn (RRID:SCR_001459) | vsn | software resource | Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. | microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
Free, Available for download, Freely available | OMICS_01977, biotools:vsn | https://bio.tools/vsn | SCR_001459 | SciCrunch Registry | vsn - Variance stabilization and calibration for microarray data | 2026-09-26 02:13:00 | 6 |
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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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