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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NIDAG: Neuroimaging Data Access Group Resource Report Resource Website |
NIDAG: Neuroimaging Data Access Group (RRID:SCR_001674) | NIDAG | data or information resource, standard specification, knowledge environment, narrative resource, international standard specification | An international working group dedicated to improving access to neuroimaging results in a free and open-access manner. It seeks to establish a universal coordinate database, including both past papers and future studies. Their current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete, this will allow anyone to find all of the articles that report a coordinate, or set of coordinates, easily and without cost. Eventually, they hope to expand this database to include not only coordinates, but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited, and also be a very useful tool for those interested in meta-analysis, and hopefully clarify structure-function relationships. They are interested in hearing from people who might be willing to contribute to their projects, particularly those with programming experience. The number of published neuroimaging studies is increasing rapidly and it is not feasible to read them all. If a computer database could store key information from published fMRI papers and make that information easier to search or share, this would have substantial benefits for the neuroimaging community. Projects like AMAT, Brainmap, Brede and SumsDB have started to tackle this problem. NIDAG wants to formalize and improve these databases so that they meet the needs of the neuroimaging community. Formal meta-analysis of published data is a valuable way to assess the consistency and reliability of experimental results. A database of neuroimaging results would facilitate meta-analyses, in conjunction with tools like GingerALE and Multi-level Kernel Density Analysis. | fmri, database, neuroimaging, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: AMAT |
Free, Freely Available | nif-0000-10161 | http://www.nitrc.org/projects/nidag | SCR_001674 | Neuroimaging Data Access Group | 2026-08-08 11:57:32 | 0 | ||||||
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ATCC Resource Report Resource Website 10000+ mentions |
ATCC (RRID:SCR_001672) | ATCC | commercial organization | Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities. | biomaterial, cell line, culture, microorganism, proteomics, protozoa, tissue, bacteria, virus, fungus, standardization, molecular genomics, reagent, yeast, microbial culture, stem cell, dna, FASEB list |
is used by: NIA Mouse cDNA Project Home Page is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: Cell Line Knowledge Base is related to: Vector Database is related to: Hyper Cell Line Database is related to: BEI Resource Repository is related to: NCBI BioSample is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: Integrated Cell Lines is related to: ATCC STR database is parent organization of: Mantle Cell Lymphoma Cell Bank works with: Cellosaurus |
Free, Freely Available | ISNI: 0000 0001 2161 7948, Wikidata: Q2843042, grid.281196.5, nif-0000-10159 | https://ror.org/03thhhv76 | SCR_001672 | ATCC: The Global Bioresource Center, American Type Culture Collection, ATCC(dna), ATCC(in host) | 2026-08-08 11:57:43 | 106588 | ||||||
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Depression Alliance Resource Report Resource Website |
Depression Alliance (RRID:SCR_001709) | data or information resource, portal, topical portal | DA works to relieve and to prevent depression by providing information and support services to those who are affected by it via their publications, supporter services and network of self-help groups for people affected by depression. Depression Alliances services help people to understand, work with and recover from symptoms associated with depression. Depression Alliance believes that the stigma and lack of accurate information surrounding depression continues to prevent people from seeking and finding appropriate and vital help when it is required. Early intervention and information are crucial in enabling those affected by depression to recover quickly and critically in preventing further episodes. Informed by the experiences of people with depression and by research, DA works extensively with government agencies and healthcare professionals to improve the service provision for those affected by depression. DA also campaigns to raise awareness amongst the general public about the realities of this severe and enduring illness by organizing a variety of events and initiatives. | depression, healthcare, information, prevention, recover, relieve, support, treatment | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10206 | SCR_001709 | DA | 2026-08-08 11:57:32 | 0 | |||||||||
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unifiedWMWqPCR Resource Report Resource Website |
unifiedWMWqPCR (RRID:SCR_001706) | software resource | Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. | standalone software, mac os x, unix/linux, windows, r, gene expression, microtitre plate assay, qpcr, differential expression, multiple comparison, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24794933 | Free, Available for download, Freely available | OMICS_03937, biotools:unifiedwmwqpcr | https://bio.tools/unifiedwmwqpcr | SCR_001706 | unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data | 2026-08-08 11:57:31 | 0 | ||||||
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rlsim Resource Report Resource Website |
rlsim (RRID:SCR_001703) | rlsim | software resource | Software package for simulating RNA-seq library preparation with parameter estimation. | rna-seq |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
Free, Available for download, Freely available | OMICS_01965 | SCR_001703 | rlsim - a package for simulating RNA-seq library preparation with parameter estimation | 2026-08-08 11:57:43 | 0 | |||||||
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Sample of Science Resource Report Resource Website |
Sample of Science (RRID:SCR_001656) | Sample of Science | journal article, data or information resource, access service resource, database, service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Free access service resource dedicated to connect researchers creating scientific samples with scientists who need samples for their experiments. With Sample of Science researchers can submit samples, or contact scientists proposing sample for dissemination. Each disseminated sample also gets its description published in Sample of Science Bulletin, a dedicated open access journal. It acquires a Digital Object Identifier (DOI) and becomes a fully citable item. Because both adequate sample descriptions and mutually-agreed dissemination conditions are key factors for a fruitful dissemination that respects mutual interest, Sample of Science provides tools to elaborate, communicate, discuss, and refine both sample description and dissemination conditions. This process, termed peer-adoption process, results in the publication of disseminated sample descriptions in Sample of Science Bulletin, a dedicated open access publication. The publication in Sample of Science Bulletin is useful to provide adequate recognition to Sample Authors who contribute to the development of science by offering visibility to their disseminated samples. To the adopter it provides experimental details regarding the sample under the form of a citable reference useful for any future publications involving this sample. To a larger scientific community interested in material science, it provides a useful tool to stay abreast the activity of sample providers in their respective field of expertise. |
nanorod, nanoprobe, imaging, biomedical, fluorescence, nanostructure, graphene, nanomaterial, magnetic material, metal-organic framework, community building portal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153937 | https://www.sampleofscience.net/ | SCR_001656 | 2026-08-08 11:57:32 | 0 | ||||||||
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RSVSim Resource Report Resource Website 10+ mentions |
RSVSim (RRID:SCR_001777) | software resource | A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates. | unix/linux, mac os x, windows, r, sequencing, structural variation |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23620362 | Free, Available for download, Freely available | OMICS_03822 | SCR_001777 | RSVSim: an R/Bioconductor package for the simulation of structural variations | 2026-08-08 11:57:44 | 16 | |||||||
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Annual Reviews: A Nonprofit Scientific Publisher Resource Report Resource Website 10+ mentions |
Annual Reviews: A Nonprofit Scientific Publisher (RRID:SCR_001655) | journal article | Annual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields. | biomedical, life science, literature, physical science, review, social science | Free, Freely Available | nif-0000-10150 | SCR_001655 | Annual Reviews | 2026-08-08 11:57:42 | 31 | |||||||||
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TCC Resource Report Resource Website 10+ mentions |
TCC (RRID:SCR_001779) | TCC | software resource | An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq). | rna-seq, differential expression, high throughput sequencing |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23837715 | Free, Available for download, Freely available | OMICS_01952 | SCR_001779 | Tag Count Comparison, TCC: Differential expression analysis for tag count data with robust normalization strategies | 2026-08-08 11:57:33 | 10 | ||||||
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Salk Institute for Biological Studies - Slesinger Lab Resource Report Resource Website |
Salk Institute for Biological Studies - Slesinger Lab (RRID:SCR_001850) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This lab is investigating the molecular details of how potassium ion channels open and close (i.e. gating), the cellular regulation of potassium channels in nerve cells, and more recently, their role in drug addiction and mental disorders. There are currently two related areas of focus in the lab. One main area of research is investigating the G protein regulation of GIRK channels, utilizing structural, biochemical and electrophysiological strategies. The other area extends from the G protein regulation experiments to studies that examine the role of GIRK channels in the neural response to drugs of abuse, utilizing biochemical, electrophysiological and behavioral strategies. | drug, electrophysiological, gating, abuse, addiction, behavioral, biochemical, cell, cellular, channel, disorder, girk channel, g protein, ion, mental, molecular, nerve, neural, potassium, regulation, structural | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10413 | SCR_001850 | Salk Institute (Slesinger) | 2026-08-08 11:57:45 | 0 | |||||||||
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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 | 2026-08-08 11:57:44 | 76 | |||||
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GenABEL Resource Report Resource Website 500+ mentions |
GenABEL (RRID:SCR_001842) | software library, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. | r, genome-wide association, single nucleotide polymorphism |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite |
Centre for Medical Systems Biology; Netherlands ; Netherlands Genomics Initiative ; Netherlands Organisation for Scientific Research ; Russian Foundation for Basic Research |
PMID:17384015 DOI:10.1186/1471-2105-11-134 DOI:10.1093/bioinformatics/btm108 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154328, OMICS_00234 | http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/, https://cran.r-project.org/web/packages/GenABEL/index.html, https://sources.debian.org/src/probabel/ | SCR_001842 | GenABEL package, R/GENABEL | 2026-08-08 11:57:33 | 506 | |||||
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FreeSurfer Resource Report Resource Website 10000+ mentions |
FreeSurfer (RRID:SCR_001847) | FreeSurfer | image analysis software, software resource, software application, data visualization software, data processing software | Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. | processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data |
is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox is used by: freesurfR is used by: Automatic Analysis is used by: NHP Freesurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian is listed by: SoftCite is related to: PySurfer is related to: RFT FDR is related to: FMRLAB is related to: TRACULA is related to: BASH4RfMRI has parent organization: Harvard University; Cambridge; United States has plug in: JOSA works with: NIAG Addiction Data |
NCRR U24 RR021382; NINDS R01 NS052585; NCRR RR014075 |
PMID:22248573 | Free, Available for download, Freely available | nif-0000-00304 | https://sources.debian.org/src/freesurfer/, http://www.nitrc.org/projects/freesurfer, http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall | SCR_001847 | 2026-08-08 11:57:45 | 12664 | |||||
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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 | 2026-08-08 11:57:33 | 0 | ||||||
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Stable Isotope Labeling with Amino Acids in Cell Culture Resource Report Resource Website 500+ mentions |
Stable Isotope Labeling with Amino Acids in Cell Culture (RRID:SCR_001873) | data or information resource, portal, topical portal | Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given "light" or "heavy" form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). In an experiment, two cell populations are grown in culture media that are identical except that one of them contains a "light" and the other a "heavy" form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%. SILAC Applications: - Differential expression of proteins and identification of disease biomarkers - Cell signaling dynamics - Analysis of yeast pheromone signaling pathway - Identification of methylation sites - Identification of protease substrates - Study of protein complexes/protein interactions - Analysis of signaling pathways and effect of pharmacological inhibitors - Subcellular proteomics Sponsors: Supported in part by an NIH Roadmap grant Technology Center for Networks & Pathways of Lysine Modification. | amino acid, analog, biomarker, cell culture, cell division, cell signal, chemical, deuterium, disease, inhibitor, in vivo, isotope, labeling, lysine, mass spectrometry, media, metabolic, methylation site, nucleus, pharmacological, protease, protein, protein complex, protein interaction, proteomics, signaling pathway, subcellular, substrate, yeast pheromone | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10435 | SCR_001873 | SILAC | 2026-08-08 11:57:35 | 673 | |||||||||
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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 | 2026-08-08 11:57:35 | 9 | |||||||
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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 | 2026-08-08 11:57:35 | 24 | ||||||
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Dendritica: Software Tools for Studying Dendritic Signaling Resource Report Resource Website 1+ mentions |
Dendritica: Software Tools for Studying Dendritic Signaling (RRID:SCR_001865) | software resource, software application, simulation software | Dendritica is a program package for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in the following paper: Vetter, P., Roth, A. & Husser, M. (2001). Action potential propagation in dendrites depends on dendritic morphology. Journal of Neurophysiology, 85: 926-937. Dendritica can functionally be divided into three main parts: - Interactive morphological analysis and electrophysiological simulation of single cells - Automated batch simulations across a set of morphologies using the same simulation parameters - Automated analysis of batch simulation runs Dendritica requires NEURON 4.1.1 with some modifications described in Appendix 1. It was tested for NEURON 4.1.1 on Linux and SGI IRIX. Some modifications to the Dendritica code may be necessary in order to run it on older or newer versions of NEURON. Sponsors: This work was supported by the Wellcome Trust, the European Community, the Max-Planck-Gesellschaft, the Wellcome Trust 4-year PhD Programme in Neuroscience. | electrophysiological simulation, dendritic geometry, interactive, morphological, morphology, neuron, sigle cell, signal propagation | Free | http://www.dendrite.org/software.html | SCR_001865 | Dendritica | 2026-08-08 11:57:33 | 1 | |||||||||
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Stony Brook University Medical Center: Neuropathology Primer Resource Report Resource Website |
Stony Brook University Medical Center: Neuropathology Primer (RRID:SCR_001866) | data or information resource, narrative resource, book | This is a primer of basic neuropathology- The Central Nervous System and Skeletal Muscle. It is organized in chapters by category of disease with a separate chapter for skeletal muscle. Many of the diseases could be included in more than one chapter because of overlapping pathophysiology; in each case the disorder is included in a single section in the interest of convenience. In order to recognize pathology one must have a basic foundation in normal structure, so the first chapter is an overview of basic regional central nervous system structure and anatomy. It includes an introduction to neurohistology. Other chapters address the pathophysiology of different categories of disease and provide examples of gross and microscopic pathology when they are available. | anatomy, central nervous system, disease, gross pathology, microscopic pathology, neurohistology, neuropathology, pathology, pathophysioogy, skeletal muscle, structure | Free, Freely available | nif-0000-10438 | http://www.stonybrookmedicalcenter.org/body.cfm?id=1176 | SCR_001866 | Neuropathology Primer | 2026-08-08 11:57:45 | 0 | ||||||||
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SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE Resource Report Resource Website 1+ mentions |
SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE (RRID:SCR_001869) | data or information resource, software resource, software application, simulation software, database | This database contains morphologies of hippocampal pyramidal cells and interneurons (in Neurolucida, NEURON, and pdf formats) as well as data recorded from those cells. Sponsors:This work was supported by grants from the NIH (T32-GM-08061 to T.J.M., F32-NS-10532 to N.L.G., and R01-NS35180 and R01-NS 46064 to N.S. and W.L.K.) and NSF (IGERT fellowship to Y.K.). NS46064 is part of the NSF/NIH Collaborative Research in Computational Neuroscience Program | cell, hippocampal, interneuron, morphology, neurolucida, neuron, pyramidal cell | Free, Freely available | nif-0000-10434 | http://www.northwestern.edu/neurobiology/faculty/spruston/sk_models/ | SCR_001869 | SPRUSTON / KATH LAB | 2026-08-08 11:57:45 | 5 |
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