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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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peak nii Resource Report Resource Website 1+ mentions |
peak nii (RRID:SCR_002572) | peak_nii | software application, software toolkit, image processing software, software resource, data processing software | Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command. | magnetic resonance, pet, spect | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Personal License | nlx_155975 | SCR_002572 | peak_nii: Statistical image clustering peak detection and data extraction, peak nii | 2026-08-11 09:40:39 | 7 | |||||||
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Wolfram Alpha Computational Knowledge Engine Resource Report Resource Website 10+ mentions |
Wolfram Alpha Computational Knowledge Engine (RRID:SCR_002693) | software application, data or information resource, database, knowledge environment, software resource | Wolfram Alpha is a computational knowledge engine that to make all systematic knowledge computable. Although, this is not a specific neuroscience related resource, the computational and math element will be helpful. Wolfram Alpha's long-term goal is to make all systematic knowledge immediately computable and accessible to everyone. It aims to collect and curate all objective data; implement every known model, method, and algorithm; and make it possible to compute whatever can be computed about anything. It's goal is to build on the achievements of science and other systematizations of knowledge to provide a single source that can be relied on by everyone for definitive answers to factual queries. Wolfram Alpha aims to also bring expert-level knowledge and capabilities to the broadest possible range of peoplespanning all professions and education levels. It's goal is to accept completely free-form input, and to serve as a knowledge engine that generates powerful results and presents them with maximum clarity. Lastly, Wolfram Alpha is an ambitious, long-term intellectual endeavor that it intends to deliver increasing capabilities over the years and decades to come. With a world-class team and participation from top outside experts in countless fields, it's goal is to create something that will stand as a major milestone of 21st century intellectual achievement. As of now, Wolfram Alpha contains 10+ trillion pieces of data, 50,000+ types of algorithms and models, and linguistic capabilities for 1000+ domains. Built with Mathematicawhich is itself the result of more than 20 years of development at Wolfram ResearchWolfram Alpha's core code base now exceeds 5 million lines of symbolic Mathematica code. Running on supercomputer-class compute clusters, Wolfram Alpha makes extensive use of the latest generation of web and parallel computing technologies, including webMathematica and gridMathematica. Its knowledge base and capabilities already span a great many domains, and its underlying framework has the power and flexibility to support ready extension to essentially any domain that is based on systematic knowledge. | element, algorithm, computational, domain, knowledge, math, method, model, neuroscience, systematic, systematization, technology | Free, Freely available | nif-0000-24917 | SCR_002693 | Wolfram Alpha | 2026-08-11 09:40:37 | 35 | |||||||||
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CTF Resource Report Resource Website 1+ mentions |
CTF (RRID:SCR_002692) | data analysis software, software application, software resource, data processing software, sequence analysis software | Conditional random field (CRF) based transcription factor binding site (TFBS) finding system. The underlying CRF model can integrate features of different sources. | conditional random field, transcription factor binding site, finding system, find transcription factor binding site |
is listed by: OMICtools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
Free, Available for download, Freely available | OMICS_00480 | SCR_002692 | 2026-08-11 09:40:35 | 1 | |||||||||
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Vaa3D Resource Report Resource Website 100+ mentions |
Vaa3D (RRID:SCR_002609) | Vaa3D, Vaa3D-Neuron | software application, data management software, software toolkit, image analysis software, software resource, data processing software, data visualization software | A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools. | reusable library, atlas application, c, c++, cygwin, fiber tracking, gnome, image display, kde, linux, macos, microsoft, magnetic resonance, neuronal characterization, development environment, position, posix/unix-like, quantification, registration, rendering, resampling, segmentation, shape analysis, spatial transformation, surface analysis, tractography, visualization, volumetric analysis, warping, win32 (ms windows), windows, windows 95/98/2000, windows nt/2000, windows vista, windows xp, 3d neuron reconstruction, 3d, neuron, reconstruction, microscopy |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Insight Segmentation and Registration Toolkit has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | Free, Available for download, Freely available | nlx_156012 | http://www.nitrc.org/projects/v3d | SCR_002609 | V3D, Vaa3D: A Swiss army knife for bioimage visualization & analysis, V3D-Neuron, Vaa3D: A Swiss army knife for bioimage visualization and analysis, 3D Visualization-Assisted Analysis, Vaa3D and Vaa3D-Neuron | 2026-08-11 09:40:40 | 166 | ||||
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FunSimMat Resource Report Resource Website 1+ mentions |
FunSimMat (RRID:SCR_002729) | FunSimMat | service resource, analysis service resource, data or information resource, database, web service, software resource, data analysis service, production service resource, data access protocol | FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online tool | functional similarity value, protein family, protein similarity, semantic similarity value, similarity value, functional similarity, disease gene candidate prioritization, disease, protein, protein family, disease candidate prioritization, semantic similarity, gene ontology, visualization, annotation, database or data warehouse |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network 01GR0453; Klinische Forschergruppe KFO 129/1-1; Klinische Forschergruppe KFO 129/1-2; European Union LSHG-CT-2003-503265 |
PMID:19923227 PMID:17932054 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02860 | SCR_002729 | FunSimMat - Functional Similarity Matrix | 2026-08-11 09:40:37 | 1 | |||||
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Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | data analysis software, software application, software resource, data processing software, sequence analysis software | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ | SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-08-11 09:40:37 | 41 | ||||||
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TractoR: Tractography with R Resource Report Resource Website 10+ mentions |
TractoR: Tractography with R (RRID:SCR_002602) | TractoR | software application, data processing software, software resource, data visualization software | Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R. | analyze, atlas application, c, dicom, linux, macos, modeling, magnetic resonance, nifti, other unix-like, posix/unix-like, quantification, r, segmentation, sh, bash, statistical operation, tractography, unix shell, visualization, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_156005 | http://www.nitrc.org/projects/tractor | SCR_002602 | Tractography with R | 2026-08-11 09:40:36 | 28 | ||||||
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PharmGKB Resource Report Resource Website 1000+ mentions |
PharmGKB (RRID:SCR_002689) | PharmGKB | service resource, data or information resource, storage service resource, database, web service, software resource, data set, data repository, data access protocol | Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed. | pharmacogenomics, microarray, pathway, phenotype, snp array, genotype, clinical, genetic variation, drug, gene, genetic variation, disease, cardiovascular, pulmonary, cancer, metabolic, transporter, drug response, small molecule, research, drug response, FASEB list |
is used by: NIF Data Federation is listed by: OMICtools is related to: WikiPathways is related to: ConsensusPathDB is related to: Integrated Molecular Interaction Database is related to: MalaCards is related to: phenomeNET has parent organization: Stanford University; Stanford; California is parent organization of: PharmGKB Ontology |
NIGMS R24 GM61374 | PMID:11908751 | Free, Freely available | nif-0000-00414, OMICS_01586, r3d100012325 | https://doi.org/10.17616/R31H1N | SCR_002689 | Pharmacogenomics Knowledge Base | 2026-08-11 09:40:37 | 1276 | ||||
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Rodent Brain WorkBench Resource Report Resource Website 10+ mentions |
Rodent Brain WorkBench (RRID:SCR_002727) | rbwb | software application, atlas, data or information resource, database, software resource, data processing software, data visualization software | The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States. | electron microscopy, image, brain, cerebellar cortex, hippocampus, connectivity, coronal section, high resolution, light microscopy, histology, microscopy, mouse brain, mouse brain atlas, mpeg, mri, nerve cell, nifti, neuroimaging, rat, rat brain, rodent brain, stereotaxic coordinate, xyz coordinate, gene expression | has parent organization: University of Oslo; Oslo; Norway | Free, Freely available | nif-0000-00424 | SCR_002727 | Rodent Brain Work Bench | 2026-08-11 09:40:36 | 21 | |||||||
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TurtleSeg Resource Report Resource Website 1+ mentions |
TurtleSeg (RRID:SCR_002605) | TurtleSeg | software application, image analysis software, software resource, segmentation software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process. | analyze, c++, computed tomography, dicom, intensity contour, microsoft, minc, magnetic resonance, nifti, segmentation, win32 (ms windows), windows, windows nt/2000, windows vista, windows xp | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156008 | http://www.nitrc.org/projects/turtleseg | SCR_002605 | TurtleSeg - Interactive 3D Image Segmentation Software | 2026-08-11 09:40:34 | 6 | ||||||
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Fungal C-values Database Resource Report Resource Website 10+ mentions |
Fungal C-values Database (RRID:SCR_002726) | service resource, data or information resource, storage service resource, database, data repository | Database for scientists interested in fungal genomics. Multiple species are included, and the database provides information on DNA C-values and genomic size. It also gives information derived from electrophoresis experiments and genome sequencing projects. The database accepts data submissions. We appreciate receiving published offprints, preprints, and personal communications providing C-value estimates for fungi. | fungal c-value, fungal genome, fungus, c-value | has parent organization: Estonian University of Life Sciences; Tartu; Estonia | PMID:17090588 | Free, Freely available | nif-0000-02857 | SCR_002726 | Fungal Genome Size Database | 2026-08-11 09:40:42 | 14 | |||||||
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GenBank Resource Report Resource Website 10000+ mentions |
GenBank (RRID:SCR_002760) | GB | service resource, data or information resource, storage service resource, database, data repository | NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP. | genetic sequence, dna sequence, human genetics, human genome, nucleotide sequence, nucleotide, dna, dna data bank, gene mapping, genetics, gold standard |
is used by: Structural Genomics Consortium is used by: xFITOM is used by: Transcriptional Regulatory Element Database is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: CINERGI is related to: High Throughput Genomic Sequences Division is related to: DNA DataBank of Japan (DDBJ) is related to: HS3D - Homo Sapiens Splice Sites Dataset is related to: Influenza Virus Resource is related to: TPA is related to: Anopheles gambiae (African malaria mosquito) genome view is related to: Nucleotide database is related to: NCBI BioSample is related to: NCBI Nucleotide is related to: SpliceDB is related to: MaizeGDB is related to: NCBI Assembly Archive Viewer is related to: DNA DataBank of Japan (DDBJ) is related to: European Molecular Biology Laboratory is related to: INSDC is related to: NCBI Protein Database is related to: TrED is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: INSDC is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables has parent organization: NCBI is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: NCBI Genome Survey Sequences Database works with: OGDraw works with: A plasmid Editor works with: Webcutter works with: merge-gbk-records works with: PremierBiosoft Proteo IQ Software works with: SARS-CoV-2-Sequences works with: rentrez works with: MiMeDB |
NLM | PMID:24217914 PMID:23193287 PMID:21071399 |
Free, Freely available | nif-0000-02873, r3d100010528, OMICS_01650 | https://doi.org/10.17616/R3D31X | SCR_002760 | , Gen Bank, GenBank | 2026-08-11 09:40:36 | 64417 | ||||
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University of Arkansas for Medical Sciences; Arkansas; USA Resource Report Resource Website 10+ mentions |
University of Arkansas for Medical Sciences; Arkansas; USA (RRID:SCR_002522) | UAMS | data or information resource, portal, organization portal, department portal | Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care. | translational medicine, public medical school |
is related to: Alzheimers Disease Genetics Consortium is related to: Clinical and Translational Science Awards Consortium has parent organization: University of Arkansas System; Arkansas; USA is parent organization of: UAMS Experimental Pathology Core Laboratory |
Free | grid.241054.6, nlx_152181, Wikidata:Q941298, Crossref funder ID:100008519, ISNI:0000 0004 4687 1637 | https://ror.org/00xcryt71 | SCR_002522 | University of Arkansas for Medical Sciences | 2026-08-11 09:40:33 | 41 | ||||||
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Coding Potential Calculator Resource Report Resource Website 100+ mentions |
Coding Potential Calculator (RRID:SCR_002764) | CPC | service resource, analysis service resource, software resource, data analysis service, production service resource | A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input. | fasta, transcript, protein coding, coding potential, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:17631615 | Free, Freely available | biotools:cpc, rid_000106 | https://bio.tools/cpc | SCR_002764 | 2026-08-11 09:40:43 | 225 | ||||||
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OpenDOAR Resource Report Resource Website 10+ mentions |
OpenDOAR (RRID:SCR_002641) | OpenDOAR | service resource, data or information resource, storage service resource, database, data repository | A quality-controlled directory of academic open access repositories that provides a simple repository list, and lets you search for repositories or search repository contents. Additionally, tools and support to both repository administrators and service providers in sharing best practice and improving the quality of the repository infrastructure are provided. The current directory lists repositories and allows breakdown and selection by a variety of criteria which can also be viewed as statistical charts. The underlying database has been designed from the ground up to include in-depth information on each repository that can be used for search, analysis, or underpinning services like text-mining. | open access, open data, repository, data sharing |
is listed by: FORCE11 is related to: DOAJ - Directory of Open Access Journals has parent organization: University of Nottingham; Nottingham; United Kingdom |
JISC | Free, Freely available | nlx_156070 | SCR_002641 | Directory of Open Access Repositories, The Directory of Open Access Repositories - OpenDOAR | 2026-08-11 09:40:37 | 40 | ||||||
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Gabi Primary Database Resource Report Resource Website 10+ mentions |
Gabi Primary Database (RRID:SCR_002755) | GABI | service resource, analysis service resource, data or information resource, storage service resource, database, data analysis service, production service resource, data repository |
Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research. GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated. * GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload. |
molecular plant physiology, plant genome, genome, blast, sequence, snp, mapping, proteomics, image collection | has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany | German Resource Center for Genome Research RZPD GmbH ; Max Planck Society ; BMBF 0312272; BMBF 0313112; BMBF 0315046 |
PMID:18812395 | Free, Freely available | nif-0000-02866, r3d100012432 | http://gabi.rzpd.de/, https://doi.org/10.17616/R3QB61 | SCR_002755 | GabiPD | 2026-08-11 09:40:37 | 13 | ||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | service resource, data or information resource, storage service resource, database, image repository, data repository | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. | microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot |
is listed by: FORCE11 is listed by: SoftCite is related to: OME-TIFF Format has parent organization: Rockefeller University; New York; USA |
Glencoe Software ; OME - Open Microscopy Environment |
PMID:22869591 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156057, r3d100010895 | https://doi.org/10.17616/R3PW4G | SCR_002633 | 2026-08-11 09:40:37 | 14 | |||||
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DSS Resource Report Resource Website 1+ mentions |
DSS (RRID:SCR_002754) | software toolkit, software resource, software library | Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. | standalone software, unix/linux, mac os x, windows, r, differential expression, rna-seq, chip-seq, dna methylation, differential expression, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24561809 | Free, Freely available, Available for download | OMICS_03273 | SCR_002754 | Dispersion Shrinakge for Sequencing data, DSS - Dispersion shrinakge for sequencing data | 2026-08-11 09:40:36 | 9 | |||||||
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pIRS Resource Report Resource Website 50+ mentions |
pIRS (RRID:SCR_002519) | software application, simulation software, software resource | Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias. | de novo data simulation, empirical distribution, illumina pair-end read, substitution sequencing error, gc depth bias | is listed by: OMICtools | PMID:22508794 | Free, Available for download, Freely available | OMICS_00254 | SCR_002519 | pIRS (profile based Illumina pair-end Reads Simulator), profile based Illumina pair-end Reads Simulator | 2026-08-11 09:40:36 | 74 | |||||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | service resource, atlas, analysis service resource, data or information resource, storage service resource, database, data analysis service, production service resource, image repository, data repository | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-08-11 09:40:43 | 14 |
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If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
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