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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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iPOP Resource Report Resource Website 10+ mentions |
iPOP (RRID:SCR_008991) | iPOP | data or information resource, data set | Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. | genomics, proteomics, transcriptional profiling, saliva, blood, maternal data, metabolomics, personalized medicine, adult human, genetics, transcriptome, male | has parent organization: Stanford University; Stanford; California | Healthy | Breetwor Family Foundation ; Korber Foundation ; Fundacion Marcelino Botin ; Fundacion Lilly ; NLM T15-LM007033; NIGMS R24-GM61374; NHLBI T32 HL094274; NHLBI KO8 HL083914; NIH New Investigator DP2 award OD004613; Spanish Ministry of Science and Innovation Projects ; Spanish Ministry of Science and Innovation Projects ; European Union FP7 Genica ; European Union FP7 TELOMARKER ; European Research Council Advanced Grant |
PMID:22424236 | Free for personal, Non-exclusive, Non-transferable, Non-commercial access., Please cite. | nlx_152492 | SCR_008991 | Snyderome, Integrated Personal Omics Profiling | 2026-09-12 01:03:18 | 14 | ||||
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Center for Computational Mass Spectrometry Resource Report Resource Website 1+ mentions |
Center for Computational Mass Spectrometry (RRID:SCR_008161) | CCMS | biomedical technology research center, training resource | Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications. | systems biology technology center, mass spectrometry, algorithm, computational proteomics, proteomics |
is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA is parent organization of: NeuroPedia |
NCRR ; NIGMS |
nlx_152677 | https://api.datacite.org/dois?prefix=10.25345 | SCR_008161 | UCSD Center for Computational Mass Spectrometry | 2026-09-12 01:03:17 | 7 | ||||||
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NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis Resource Report Resource Website 1+ mentions |
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) | Mass Spectrometry Resource, WU Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry | systems biology technology center, mass spectrometry, protein, lipid, metaboilite, biomarker, isotope, analysis | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIGMS ; NCRR 2P41RR00954 |
nlx_152688 | SCR_009009 | Mass Spectrometry Resource at Washington University in St. Louis, Washington University Mass Spectrometry Resource | 2026-09-12 01:03:18 | 1 | |||||||
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Resource for Integrated Glycotechnology Resource Report Resource Website |
Resource for Integrated Glycotechnology (RRID:SCR_009008) | Resource for Integrated Glycotechnology | biomedical technology research center, training resource | Biomedical technology research center that develops technologies to increase understanding of the molecular basis of the involvement of carbohydrates in protein-carbohydrate interactions in disease and to develop more powerful technologies necessary to achieve this goal. Complex carbohydrates play an important role in many biomedically important processes, including inflammatory response, hormone action, malignancy, viral and bacterial infections and cell differentiation. The resource combines complimentary technologies: synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression and cell-based assays. As new technologies are developed, application to these processes will be pursued through collaborative and service projects. | systems biology technology center, protein-carbohydrate interaction, disease, synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression, cell-based assay, glycan, enzyme, carbohydrate | has parent organization: University of Georgia; Georgia; USA | NIGMS 8 P41 GM103390-23; NCRR 5P41RR005351-23 |
nlx_152685 | SCR_009008 | 2026-09-12 01:03:18 | 0 | ||||||||
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National Resource for Biomedical Accelerator Mass Spectrometry Resource Report Resource Website |
National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) | Resource for Biomedical AMS | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers. | systems biology technology center, accelerator mass spectrometry, radioisotope, isotope | has parent organization: Lawrence Livermore National Laboratory | NCRR ; NIGMS |
nlx_152682 | SCR_009006 | 2026-09-12 01:03:18 | 0 | ||||||||
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Integrated Technology Resource for Biomedical Glycomics Resource Report Resource Website 1+ mentions |
Integrated Technology Resource for Biomedical Glycomics (RRID:SCR_009003) | Integrated Technology Resource for Biomedical Glycomics | biomedical technology research center, training resource | Biomedical technology research center that develops and implements new technologies to investigate the glycome of cells, including glycoproteomics and glycoconjugate analysis, transcript analysis and bioinformatics. It develops the tools and technology to analyze in detail the glycoprotein and glycolipid expression of mouse embryonic stem cells and the cells into which they differentiate. The technology developed in the Center will allow an understanding of how glycosylation is controlled during differentiation and will allow the development of tools to promote the use of stem cells to treat human disease. In addition, the technology developed will be applicable to the study of other cell types, including cancer cells that are progressing to a more invasive phenotype. The technology developed will also allow others in the scientific community to participate in glycomics research through dissemination of the new methods developed and through the analytical services provided by the resource to other scientists requesting assistance in glycomic analyses. | systems biology technology center, glycome, cell, glycoproteomics, glycoconjugate analysis, transcript analysis, bioinformatics, glycoprotein, glycolipid, embryonic stem cell, glycosylation, stem cell, glycomics | has parent organization: University of Georgia; Georgia; USA | NCRR ; NIGMS |
nlx_152678 | SCR_009003 | NCRR Integrated Technology Resource for Biomedical Glycomics | 2026-09-12 01:03:18 | 1 | |||||||
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SSRL Structural Molecular Biology Resource Report Resource Website 1+ mentions |
SSRL Structural Molecular Biology (RRID:SCR_009000) | SSRL SMB | biomedical technology research center, training resource | Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis. | synchrotron, radiation, structural biology, structural biology technology center, macromolecular crystallography, x-ray absorption spectroscopy, small-angle x-ray scattering, diffraction | has parent organization: Stanford University; Stanford; California | DOE ; NIGMS ; NCRR P41RR001209 |
nlx_152676 | SCR_009000 | Stanford Synchrotron Radiation Lightsource Structural Molecular Biology, Synchrotron Radiation Structural Biology Resource | 2026-09-12 01:03:18 | 1 | |||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, software resource, source code | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIGMS R01 GM078598; NIMH R01 MH101244 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE, http://genetics.bwh.harvard.edu/cbase | SCR_027765 | Cancer Bayesian SElection estimation | 2026-09-12 01:05:36 | 0 | |||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, software resource, software toolkit, source code | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NCI R01 CA227388; NCI R37 CA222574; NCI U01 CA233100; NIGMS T32 GM008313; NSF |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | 2026-09-12 01:05:35 | 4 | |||||||||
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HiTIMED Resource Report Resource Website |
HiTIMED (RRID:SCR_028180) | software application, software resource, source code | Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens. | estimate cell proportions, cell type resolution, tumor microenvironment, tumor-type-specific DNA methylation data, | NCI P30 CA168524; NCI P50 CA097257; NCI R01 CA207360; NCI R01CA216265; NIGMS P20 GM130423; NIGMS P20GM103428; NIGMS P20GM104416 |
PMID:36348337 | Free, Available for download, Freely available | SCR_028180 | Hierarchical Tumor Immune Microenvironment Epigenetic Deconvolution | 2026-09-12 01:05:45 | 0 | ||||||||
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OncoDB Resource Report Resource Website 50+ mentions |
OncoDB (RRID:SCR_028340) | data or information resource, database | Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival. | cancer patients data, gene expression, DNA methylation, somatic mutations, proteomic profiles, chromatin accessibility, | NCI R01CA287778; NIDCR R01DE026471; NIGMS R35GM141535 |
PMID:34718715 PMID:40995640 |
Free, Freely available, | SCR_028340 | OncoDB2.0 | 2026-09-12 01:05:48 | 84 | ||||||||
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Conditional AutoRegressive Deconvolution Resource Report Resource Website 1+ mentions |
Conditional AutoRegressive Deconvolution (RRID:SCR_026310) | CARD | software resource, software toolkit, source code | Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations. | Deconvolution method, spatial transcriptomics, cell-type-specific expression, single-cell RNA sequencing, cell-type composition across tissue locations, | NHGRI R01HG011883; NIGMS R01GM126553; NIGMS R01GM144960 |
PMID:35501392 | Free, Available for download, Freely available | SCR_026310 | , CARD: Conditional AutoRegressive Deconvolution, Conditional autoregressive-based deconvolution | 2026-09-12 01:05:02 | 3 | |||||||
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AutoDockTools Resource Report Resource Website 1000+ mentions |
AutoDockTools (RRID:SCR_026401) | ADT | software application, software resource | Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. | automated docking, selective receptor flexibility, predict binding, bind to receptor of known 3D structure, ligand, analyze dockings | NIGMS RO1 GM069832 | PMID:19399780 | Free, Available for download, Freely available | https://autodock.scripps.edu/ | SCR_026401 | AutoDockTools: the Graphical User Interface for AutoDock | 2026-09-12 01:05:03 | 2063 | ||||||
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NucleAIzer Resource Report Resource Website 1+ mentions |
NucleAIzer (RRID:SCR_026500) | software resource, source code | Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool. | nucleus segmentation, image style transfer, | Academy of Finland ; European Regional Development Funds ; NIGMS R35 GM122547; Swedish Research Council |
DOI:10.1016/j.cels.2020.04.003 | Free, Available for download, Freely available | SCR_026500 | 2026-09-12 01:05:05 | 4 | |||||||||
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MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | software resource, software toolkit, source code | Software package for finding the location of m6A sites in MeRIP-seq data. | finding location of m6A sites, MeRIP-seq data | Natural Science Foundation of China ; NCI P30CA54174; NCI U54 CA113001; NIGMS R01 GM113245; NSF |
PMID:27307641 | Free, Available for download, Freely available | SCR_026533 | 2026-09-12 01:05:06 | 11 | |||||||||
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Liftoff Resource Report Resource Website 10+ mentions |
Liftoff (RRID:SCR_026535) | software resource, source code | Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations. | Aligns genes, reference genome to target genome alignment, mapping of gene annotations, genome annotation lift-over, mapping genes between two assemblies of species, mapping genes, same or closely related species, | NHGRI R01 HG006677; NIGMS R35 GM130151 |
PMID:33320174 | Free, Available for download, Freely available | SCR_026535 | 2026-09-12 01:05:06 | 10 | |||||||||
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EndoMap Resource Report Resource Website 1+ mentions |
EndoMap (RRID:SCR_026690) | data or information resource, database | Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes. | Structural protein interactome, structural interactome viewer, endosomal protein-protein interactions, human early endosomes, | Aligning Science Across Parkinson ; Michael J Fox Foundation ; NIGMS RO1 GM132129; NINDS R01NS110395 |
DOI:10.1101/2025.02.07.636106 | Free, Freely available | SCR_026690 | EndoMAP.v1 | 2026-09-12 01:05:10 | 2 | ||||||||
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kraken2 Resource Report Resource Website 1000+ mentions |
kraken2 (RRID:SCR_026838) | software application, software resource, source code | Software tool as second version of Kraken taxonomic sequence classification system. | taxonomic sequence classification system, taxonomic, sequence, classification system, | NIGMS R01 GM118568; NIGMS R35 GM130151; NSF |
PMID:31779668 | Free, Available for download, Freely available | SCR_026838 | 2026-09-12 01:05:13 | 1421 | |||||||||
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apeglm Resource Report Resource Website 1+ mentions |
apeglm (RRID:SCR_026951) | software resource, software toolkit | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NCI P01 CA142538; NHGRI R01 HG009125; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-09-12 01:05:15 | 2 | ||||||||
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PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | 3d visualization software, data processing software, data visualization software, software application, software resource, source code | Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances. | visualizing high dimensional data, high dimensional data, | NHGRI 1R01HG008383; NICHD F31HD097958; NIGMS R01GM107092; NIGMS R01GM130847; NSF |
PMID:31796933 | Free, Available for download, Freely available, | SCR_027119 | Potential of Heat-diffusion for Affinity-based Transition Embedding | 2026-09-12 01:05:19 | 5 |
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