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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EchoMRI Resource Report Resource Website 10+ mentions |
EchoMRI (RRID:SCR_017104) | instrument supplier, material resource | International research instruments company that develops, manufactures and markets NMR and CT-based whole body composition and tissue characterization equipment. | Commercial, international, research, instrument, echo, medical, system, company, NMR, CT scan, whole, body, composition, tissue, analysis | SCR_017104 | EchoMRI™ | 2026-07-25 12:14:18 | 20 | |||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Medicinal Chemistry Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Medicinal Chemistry Facility (RRID:SCR_014872) | instrument supplier, material resource | Core facility that provides general synthetic and medicinal chemistry resources and expertise to the biomedical research community. Services include chemistry consulting for projects, grant applications, synthetic chemistry, medicinal chemistry, and analytical chemistry, as well as access to equipment for synthesis, purification, and analysis. | facility, la jolla, medicinal chemistry, synthesis, analysis, grant application, consultation | Commercially available | SCR_014872 | SBP Medicinal Chemistry Facility, SBP Medical Discovery Institute Medicinal Chemistry Facility | 2026-07-25 12:14:04 | 0 | ||||||||||
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Thermo Fisher: Ion Torrent Genexus Integrated Sequencer Resource Report Resource Website 1+ mentions |
Thermo Fisher: Ion Torrent Genexus Integrated Sequencer (RRID:SCR_026449) | instrument resource | Ion Torrent Genexus Integrated Sequencer is part of the Ion Torrent Genexus System. Instrument that can automate library construction, templating, and sequencing in single-instrument run. | sequencer, automate NGS library preparation, sequencing, analysis | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_026449.pdf | Model_Number_Genexus | SCR_026449 | Genexus Integrated Sequencer | 2026-07-25 12:15:23 | 1 | |||||||||
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FEI: Helios Nanolab 600i DualBeam Resource Report Resource Website |
FEI: Helios Nanolab 600i DualBeam (RRID:SCR_027033) | instrument resource | Scanning Electron Microscope advanced DualBeam for ultra-high resolution imaging, analysis and fabrication at the nanoscale. Helios NanoLab 600i builds on the success of FEI’s winning DualBeam series offering advances in ion beam, electron beam, patterning and range of features to make milling, imaging, analysis and sample preparation down to nanoscale. | Scanning Electron Microscope, imaging, analysis, nanoscale, microscope, electron microscope, | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_027033.pdf | Model_Number_Helios_NanoLab_600i | SCR_027033 | FEI Helios NanoLab 600i DuaBeam, , FEI Helios NanoLab 600i DuaBeam Scanning Electron Microscope, Helios NanoLab 600i | 2026-07-25 12:15:33 | 0 | |||||||||
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Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis (RRID:SCR_014851) | biomaterial supply resource, material resource | Animal imaging and analysis lab that provides imaging and analytical services for SBP investigators. The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies. Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood. | animal, facility, imaging, analysis, in vivo, non invasive, luminescence imaging, fluorescence imaging, tumor, metastasis, complete blood cell count, cbc, serum, organic, mouse, blood | Commercially available | SCR_014851 | SBP Animal Imaging and Analysis, SBP Medical Discovery Institute Animal Imaging and Analysis | 2026-07-25 12:12:58 | 0 | ||||||||||
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The Cancer Genome Atlas Resource Report Resource Website 5000+ mentions |
The Cancer Genome Atlas (RRID:SCR_003193) | TCGA | biomaterial supply resource, material resource | Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments. * Genome Data Analysis Centers (GDACs) - Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data. TCGA is actively developing a network of collaborators who are able to provide samples that are collected retrospectively (tissues that had already been collected and stored) or prospectively (tissues that will be collected in the future). | genome, genome sequencing, breast, central nervous system, endocrine, gastrointestinal, gynecologic, head, neck, hematologic, skin, soft tissue, thoracic, urologic, clinical, genomic characterization, analysis, tumor genome, demographic, gene expression, copy number alteration, epigenetic, dna sequence, exome, snp, methylation, mrna, mirna, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: BioXpress is used by: cancerRxTissue is listed by: One Mind Biospecimen Bank Listing is related to: Cancer3D is related to: Cancer Research Data Commons is related to: CancerMIRNome is related to: Broad Institute Genomics Platform has parent organization: National Cancer Institute works with: FireBrowse |
Cancer, Tumor, Normal, Breast cancer, Central Nervous System cancer, Endocrine cancer, Gastrointestinal cancer, Gynecologic cancer, Head cancer, Neck cancer, Hematologic cancer, Skin cancer, Soft tissue cancer, Thoracic cancer, Urologic cancer | NCI 261200800001E-12-0-1 | nlx_156913 | SCR_003193 | Cancer Genome Atlas | 2026-07-25 12:12:27 | 6292 | ||||||
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Vanderbilt X-Ray Photoelectron Spectroscopy Lab Resource Report Resource Website |
Vanderbilt X-Ray Photoelectron Spectroscopy Lab (RRID:SCR_000897) | instrument supplier, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Lab with access to the PHI Versaprobe, a surface-sensitive analytical tool for identifying elemental composition and local bonding environment. | versaprobe, elemental composition, local bonding, environment, analysis, photoelectron, spectroscopy, xps |
is listed by: Eagle I has parent organization: Vanderbilt University; Tennessee; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156680 | http://eagle-i.ea.vanderbilt.edu/i/00000138-7b9d-06cc-480b-864680000000 | SCR_000897 | 2026-07-25 12:13:18 | 0 | ||||||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-07-26 09:06:37 | 4 | ||||
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Metafer Resource Report Resource Website 10+ mentions |
Metafer (RRID:SCR_016306) | software application, software resource | Software application to control the slide scanning hardware in Metasystem scanning and imaging platform used for automated image analysis applications in cytogenetics, hematology, pathology, toxicology, forensic sciences or microbiology microscopy. Optimized for clinical routine. | Metasystem, slide, scanning, image, automate, analysis, microscopy, life, science | Commercially available | SCR_016306 | 2026-07-26 09:06:38 | 16 | |||||||||||
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Lab Streaming Layer Resource Report Resource Website 50+ mentions |
Lab Streaming Layer (RRID:SCR_017631) | LSL | software application, software resource | System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording. | Synchronizing, streaming, data, live, analysis, recording, collection, time, series, EEG | has parent organization: University of California at San Diego; California; USA | Army Research Laboratory ; NINDS R01 NS047293 |
Free, Freely available | SCR_017631 | Lab Streaming Layer | 2026-07-26 09:07:06 | 67 | |||||||
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QGIS Resource Report Resource Website 100+ mentions |
QGIS (RRID:SCR_018507) | software application, software resource | Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps. | Geographic information system, viewing, editing, analysis, geospatial data, spatial information analysis, graphical map, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:QGIS | https://bio.tools/QGIS | SCR_018507 | 2026-07-26 09:07:14 | 400 | ||||||||
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IgBLAST Resource Report Resource Website 500+ mentions |
IgBLAST (RRID:SCR_002873) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine. | gene, analysis, domain, homology, immunoglobulin v, nucleotide, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: NCBI |
PMID:23671333 | Free, Freely available | nif-0000-25554, biotools:igblast, OMICS_06083 | https://bio.tools/igblast, https://sources.debian.org/src/ncbi-igblast/ | SCR_002873 | IgBLAST | 2026-07-26 09:03:23 | 609 | ||||||
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SBIA Resource Report Resource Website 1+ mentions |
SBIA (RRID:SCR_013628) | SBIA | access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher. | effect, alzheimer's, analysis, anatomical, biomedical, biophysical, brain, cancer, breast cancer, cardiac, classification, clinical, computer, deformation, dimensional, disease, method, model, mouse, organ, pattern, prostate, registration, schizophrenia, segmentation, statistical analysis, study, treatment, image | has parent organization: University of Pennsylvania; Philadelphia; USA | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-33052 | SCR_013628 | The Section for Biomedical Image Analysis, Section for Biomedical Image Analysis | 2026-07-26 09:05:57 | 4 | |||||||
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RDPipeline Resource Report Resource Website 10+ mentions |
RDPipeline (RRID:SCR_001192) | RDPipeline | software application, software resource, data processing software | Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available. | amplicon sequencing, high-throughput sequencing, rrna, assembly, quality filtering, taxonomy, analysis, FASEB list |
is listed by: OMICtools has parent organization: Ribosomal Database Project |
PMID:24288368 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02158 | SCR_001192 | RDP Pipeline, RDP Amplicon Sequence Pipeline | 2026-07-26 09:02:55 | 39 | ||||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | software application, software resource, data processing software | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-07-26 09:03:58 | 120 | |||||
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Gene Expression Profile Analysis Suite Resource Report Resource Website 10+ mentions |
Gene Expression Profile Analysis Suite (RRID:SCR_008341) | software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. | expression, gene, analysis, genomic, microarray, microarray platform, prediction, data set |
is listed by: 3DVC has parent organization: Principe Felipe Research Centre; Valencia; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25201 | SCR_008341 | Gepas | 2026-07-26 09:04:35 | 20 | ||||||||
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CURRY Resource Report Resource Website 100+ mentions |
CURRY (RRID:SCR_009546) | CURRY | software application, software resource, data processing software | Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package. | multimodal, atlas, application, connectivity, analysis, computed, tomography, database, eeg, meg, electrocorticography, modeling, finite, element, format, conversion, forward, inverse, image, reconstruction, meg, mesh, generation, model, magnetic resonance, pet, spect, segmentation, simulation, spatial, transformation, volumetric, neuroimaging, FASEB list | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155726 | http://www.nitrc.org/projects/curry_7 | SCR_009546 | CURRY Scan 7 Neuroimaging Suite, CURRY 8, CURRY 7, CURRY Neuroimaging Suite | 2026-07-26 09:04:53 | 160 | ||||||
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Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, software resource, data processing software | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-07-26 09:07:02 | 59 | ||||||
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Template Based Rotation Resource Report Resource Website 1+ mentions |
Template Based Rotation (RRID:SCR_012157) | TBR | software application, image analysis software, software resource, data processing software | A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations. | functional connectivity, analysis, fmri, fcmri, parcellation, map, template, resting state, matlab | Aging | NIA P01AG036694 | DOI:10.1016/j.neuroimage.2014.08.022 | GNU General Public License v3 | rid_000095 | http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/Aarons_Scripts.html | SCR_012157 | Template Based Rotation (TBR) | 2026-07-27 09:34:03 | 1 | ||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | software application, image analysis software, software resource, data processing software | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-07-27 09:35:15 | 13 |
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