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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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National Resource for the Mass Spectrometric Analysis of Biological Macromolecules Resource Report Resource Website |
National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) | National Resource for the Mass Spectrometric Analysis of Biological Macromolecules | biomedical technology research center, training resource | Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available. | systems biology technology center, mass spectrometric, analysis, peptide, protein, software, proteomic, cellular function | has parent organization: Rockefeller University; New York; USA | NIGMS | nlx_152683 | SCR_009007 | 2026-09-12 01:03:18 | 0 | ||||||||
|
scVelo Resource Report Resource Website 100+ mentions |
scVelo (RRID:SCR_018168) | software resource, software toolkit | Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling. | RNA veloscity, analysis, single cell, dynamic modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:scVelo | https://scvelo.readthedocs.io/, https://bio.tools/scVelo | SCR_018168 | scvelo, single-cell RNA Velocity generalized to transient cell states | 2026-09-12 01:02:55 | 246 | |||||||
|
Scrattch.Hicat Resource Report Resource Website 10+ mentions |
Scrattch.Hicat (RRID:SCR_018099) | data analytics software, software application, software resource | Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute. | Hierarchical, iterative clustering, analysis, transcriptomics, data, single cell RNAseq, Allen Institute | has parent organization: Allen Institute | Free, Available for download, Freely available | SCR_018099 | Scrattch Hierarchical, Iterative Clustering for Analysis of Transcriptomics | 2026-09-12 01:02:55 | 32 | |||||||||
|
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 | 2026-09-12 01:02:56 | 488 | ||||||||
|
maser Resource Report Resource Website 1+ mentions |
maser (RRID:SCR_023484) | software resource, software toolkit | Software package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events. Mapping alternative splicing events to proteins. | Mapping alternative splicing events to proteins, alternative splicing events, analysis, annotation, visualizaton | Free, Available for download, Freely available | https://bioconductor.org/packages/maser/ | SCR_023484 | Mapping Alternative Splicing Events to pRoteins | 2026-09-12 01:03:04 | 7 | |||||||||
|
Donald Danforth Plant Science Center Bioanalytical Chemistry Facility Resource Report Resource Website 1+ mentions |
Donald Danforth Plant Science Center Bioanalytical Chemistry Facility (RRID:SCR_001047) | access service resource, core facility, service resource | Facility provides tools for high quality plant and biological sample analysis in proteomics, mass spectrometry, metabolomics, ionomics, and related analytical fields. It works with academic and commercial institutions and has established collaborations with many principle investigators. | Plant, sample, analysis, proteomics, mass spectrometry, metabolomics, ionomics, elemental profiling |
is listed by: ABRF CoreMarketplace has parent organization: Donald Danforth Plant Science Center |
Restricted | ABRF_194 | https://coremarketplace.org/?FacilityID=194 | http://www.scienceexchange.com/facilities/proteomics-and-mass-spectrometry-facility, https://www.danforthcenter.org/scientists-research/core-technologies/proteomics-mass-spectrometry | SCR_001047 | Danforth Center Proteomics and Mass Spectrometry Facility, Donald Danforth Plant Science Center Proteomics and Mass Spectrometry Facility, Proteomics and Mass Spectrometry Facility, Danforth Center Ionomics, Danforth Center Mass Spectrometry Facility, Danforth Center Proteomics Facility | 2026-09-12 01:03:11 | 1 | ||||||
|
UAlbany Proteomics Core Facility Resource Report Resource Website |
UAlbany Proteomics Core Facility (RRID:SCR_001048) | access service resource, core facility, service resource | A core facility that provides services in the identification of individual proteins, characterization of entire protein complexes or biosimilars, and global analysis to discover changes in the proteomes of different samples. The core also specializes in the development of custom assays for quantitation of specific molecules in complex clinical samples. | proteins, biosimilars, analysis, proteomics, core facility, custom assays, quantitation |
is listed by: ScienceExchange has parent organization: University at Albany Center for Functional Genomics |
Available to the research community, Fee-for-service basis, Available to investigators at the University at Albany, Available to academic institutions, Available to commercial entities | SciEx_537 | http://www.scienceexchange.com/facilities/proteomics-core-facility-ualbany | SCR_001048 | UAlbany CFG Proteomics Core Facility, University at Albany CFG Proteomics Core Facility, University at Albany Center for Functional Genomics Proteomics Core Facility | 2026-09-12 01:03:11 | 0 | |||||||
|
VectorFriends Resource Report Resource Website |
VectorFriends (RRID:SCR_001230) | VectorFriends | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists. | cloning, isothermal assembly, pcr, primer design, data management, sequence analysis, sequence, analysis, primer, windows, mac os | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02113 | SCR_001230 | 2026-09-12 01:03:11 | 0 | ||||||||
|
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 | 2026-09-12 01:03:10 | 0 | ||||||||
|
Proteomics Research Center for Integrative Biology Resource Report Resource Website |
Proteomics Research Center for Integrative Biology (RRID:SCR_001098) | Proteomics Resource for Integrative Biology | biomedical technology research center, training resource | Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use. | systems biology technology center, proteomics, mass spectrometry, data management, analysis | has parent organization: Pacific Northwest National Laboratory | NIGMS 4P41GM103493-14 | nlx_152684 | SCR_001098 | Proteomics Research Resource for Integrative Biology | 2026-09-12 01:03:11 | 0 | |||||||
|
Resource for Biocomputing Visualization and Informatics Resource Report Resource Website 100+ mentions |
Resource for Biocomputing Visualization and Informatics (RRID:SCR_001374) | RBVI | biomedical technology resource center, training resource | Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas. | training resource, molecular modeling, software, molecular graphics, visualization, modeling, molecular structure, analysis, computation, computing and informatics technology center, FASEB list |
is listed by: 3DVC has parent organization: University of California at San Francisco; California; USA is parent organization of: Structure-function linkage database is parent organization of: UCSF Chimera |
NIGMS | nlx_152531 | SCR_001374 | 2026-09-12 01:03:11 | 158 | ||||||||
|
Center for Functional Neuroimaging Technologies Resource Report Resource Website 1+ mentions |
Center for Functional Neuroimaging Technologies (RRID:SCR_001423) | CFNT | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center that develops and applies innovative neuroimaging technologies and techniques to enable closer examination of the human brain, and thereby contribute to better understanding of the brain in health and disease. They develop new techniques and advance existing technologies for acquisition and analysis of functionally specific images of the working brain, with unprecedented physiological precision and spatiotemporal resolution. The research and development aims to improve and extend existing methods for non-invasive magnetic resonance image analysis and acquisition, electromagnetic source imaging, optical neuroimaging, and most recently, combined MR-PET neuroimaging. The Resource provides an essential interactive environment, within which an interdisciplinary team of highly skilled scientists, engineers, and clinicians with diverse expertise in multiple modalities and disciplines. The resource supports service use of the Center's facilities by neuroscientists throughout the country, provide extensive training opportunities for students, fellows, and staff scientists, and seek to advance the field of brain mapping through active dissemination of new knowledge and technology. | mri, neuroimaging, pet, acquisition, analysis, brain, electromagnetic source imaging, optical neuroimaging, multimodal, magnetic resonance, eeg, meg, electrocorticography, information resource, optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
NIBIB 5P41EB015896-18 | Free, Available for download, Freely available | nlx_152644 | http://www.nitrc.org/projects/cfnt | SCR_001423 | 2026-09-12 01:03:11 | 1 | ||||||
|
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 | 2026-09-12 01:02:51 | 0 | ||||||||||
|
QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | data analytics software, software application, software resource | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool, https://bio.tools/qmrlfs-finder | SCR_014584 | QmRLFS finder | 2026-09-12 01:02:51 | 16 | |||||
|
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 |
NCRR KL2 RR029885; NIDDK P01 DK056492; NIDDK R01 DK088541; NIDDK RC4DK090860; NIGMS P50 GM071558; NLM RC2 LM010994 |
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 | 2026-09-12 01:02:53 | 6 | ||||
|
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 | 2026-09-12 01:02:53 | 17 | |||||||||||
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metagear Resource Report Resource Website |
metagear (RRID:SCR_017085) | software resource, software toolkit | Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis. | sythesis, taxonomy, systematic, review, assemble, screen, literature, extract, meta, data, analysis, statistical |
is listed by: CRAN is related to: R Project for Statistical Computing has parent organization: University of South Carolina; South Carolina; USA |
NSF DBI-1262545; NSF DEB-1451031 |
DOI:10.1111/2041-210X.12472 | Free, Available for download, Freely available | https://github.com/cran/metagear, https://lajeunesse.myweb.usf.edu | SCR_017085 | 2026-09-12 01:02:54 | 0 | |||||||
|
CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-09-12 01:02:54 | 1908 | ||||||
|
Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
Austrian Science Fund J-3401; Dutch Brain Foundation ; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NHGRI F32HG007805; NHGRI HG007022; NHGRI R01 HG006399; NHLBI HL117626; NIMH R01 MH101244; NWO 480-05-003; Wellcome Trust WT098051 |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-09-12 01:02:53 | 57 | |||||
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Neurolucida Explorer Resource Report Resource Website 100+ mentions |
Neurolucida Explorer (RRID:SCR_017348) | data analytics software, software application, software resource | Companion analytical software for Neurolucida and Neurolucida 360, designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions, and brain maps. | Morphometric, analysis, neuron, reconstruction, section, brain, map, mbfbioscience, MBF Bioscience | SCR_017348 | 2026-09-12 01:02:54 | 116 |
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