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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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South Carolina Medical University Mass Spectrometry Core Facility Resource Report Resource Website 1+ mentions |
South Carolina Medical University Mass Spectrometry Core Facility (RRID:SCR_017959) | access service resource, core facility, service resource | Core provides expertise, services, education, and instrumentation to enhance biomedical research through LC-MS/MS-based proteomics. Services are offered for protein identification; characterization of post-translational modifications; and quantitative proteomics to identify differentially expressed/degraded proteins, regulated sites of post-translational modification, protein-protein interactions, and protein targets of drugs identified in phenotypic screens. Analyses include sample preparation, LC-MS/MS, database searching, generation of reports, and assistance with data interpretation. Faculty and staff assist with experimental design and development/optimization of customized methodology for analysis of post-translationally modified peptides (e.g. phosphorylation and O-GlcNAc modification, N- and O-linked glycosylation, Cys modifications including S-glutathionylation, and glycation of Lys and Arg). Quantitative approaches including metabolic labeling (SILAC), isobaric tagging (iTRAQ/TMT), and label free proteomics (LFQ) are performed on Orbitrap Elite or Orbitrap Fusion Lumos Mass Spectrometers. Developes methodology to identify alterations in post-translational modifications that impact signal transduction, transcription, translation, and response to therapeutics with goal of enabling investigators to discover molecular mechanisms underlying disease progression and therapeutic response. | Mass, spectrometry, expertise, service, education, instrumentation, proteomics, protein, identification, characterization, post translational, modification, target, drug, identification, phenotypic, screen, analysis, disease, service, core, ABRF | is listed by: ABRF CoreMarketplace | NIGMS P20 GM103542; NIH Office of the Director S10 OD010731 |
ABRF_985 | SCR_017959 | MUSC Mass Spectrometry Facility | 2026-09-12 01:04:06 | 1 | ||||||||
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Vermont University Proteomics Core Facility Resource Report Resource Website 10+ mentions |
Vermont University Proteomics Core Facility (RRID:SCR_018667) | access service resource, core facility, service resource | Provides central resource of mass spectrometry based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. Provides mass spectrometry expertise for analyzing proteins and peptides for proteomics studies, support for data analysis from proteomics measurements, training in proteomics methods, and experimental design. | USEDit, mass spectrometry, proteomics technology, protein, biomedical sample, protein analysis, peptide, measurement, experimental design, ABRF | is listed by: ABRF CoreMarketplace | NIGMS P20 GM103449 | Open | ABRF_44 | https://coremarketplace.org/?FacilityID=44 | https://vgn.uvm.edu/proteomics/ | SCR_018667 | UVM-Proteomics Facility, University of Vermont Proteomics Facility | 2026-09-12 01:04:07 | 14 | |||||
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University of New Hampshire University Instrumentation Center Core Facility Resource Report Resource Website |
University of New Hampshire University Instrumentation Center Core Facility (RRID:SCR_021101) | UIC | access service resource, core facility, service resource | University wide core facility offers NMR,SEM including FIB, EBS, EBSD, Tensile Stage,Confocal,X-Ray Photoelectron Spectroscopy,X-Ray Microscope aka Micro CT, Expert analysis of research and industrial samples,Training in scientific instrument operation and data analysis, Maintenance, repair, and calibration of instruments,Specialty instrument engineering design and application services,Facilitation of access to scientific instruments throughout the university. | USEDit, ABRF, ABRF | is listed by: ABRF CoreMarketplace | NIGMS GM113131; NSF 1337897; NSF 1429282; NSF 1828319; NSF OIA 1757371 |
open | ABRF_640 | https://coremarketplace.org/?FacilityID=640 | SCR_021101 | University Instrumentation Center, University of New Hampshire University Instrumentation Center | 2026-09-12 01:04:10 | 0 | |||||
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PEPATAC Resource Report Resource Website 1+ mentions |
PEPATAC (RRID:SCR_024758) | software resource, software toolkit | Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats. | ATAC-seq analysis pipeline, ATAC-seq data, analysis, serial alignments, | American Society of Hematology ; Howard Hughes Medical Institute ; NHGRI RM1 HG007735; NIGMS R35 GM128636 |
PMID:34859208 | Free, Available for download, Freely available | https://github.com/databio/PEPATAC/releases | SCR_024758 | 2026-09-12 01:04:30 | 2 | ||||||||
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CellMinerCDB Resource Report Resource Website 10+ mentions |
CellMinerCDB (RRID:SCR_025649) | software resource, web application | Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements. | integrating cancer cell line pharmacogenomics, exploration and analysis of cancer cell line pharmacogenomic data, exploration and analysis, cancer cell line, pharmacogenomic data | is used by: National Cancer Institute Genomics and Pharmacology Core Facility | NCI ; NIGMS P41 GM103504 |
PMID:30553813 PMID:30553813 |
Free, Freely available, | SCR_025649 | , Cell Miner CDB, CellMiner Cross-Database, CellMinerCDB 1.2 | 2026-09-12 01:04:49 | 18 | |||||||
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BioXTAS RAW Resource Report Resource Website 50+ mentions |
BioXTAS RAW (RRID:SCR_025769) | software application, software resource | Software tool as GUI based Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data.Small-angle scattering data reduction and analysis. Available on Windows, macOS (and OS X), and Linux. | reduction and analysis of small-angle X-ray solution scattering data, small-angle X-ray solution scattering data, | NIGMS P30 GM138395; US Department of Energy |
PMID:29021737 PMID:38322719 |
Free, Freely available, | SCR_025769 | BioXTAS RAW 2 | 2026-09-12 01:04:51 | 63 | ||||||||
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Intercellular Junction Organization Quantification Resource Report Resource Website 1+ mentions |
Intercellular Junction Organization Quantification (RRID:SCR_026026) | IJOQ | data analysis software, data processing software, software application, software resource, source code | Software Python tool for fully automated analysis of cell-cell junction integrity. Used for fluorescence microscopy analysis. | automated analysis, cell-cell junction integrity, fluorescence microscopy analysis, | California State University Program for Education and Research in Biotechnology Graduate Student COVID-19 Research Restart Program ; NIGMS 1SC2GM141988 |
PMID:35755841 | Free, Available for download, Freely available | SCR_026026 | 2026-09-12 01:04:56 | 1 | ||||||||
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Mustache Resource Report Resource Website 1+ mentions |
Mustache (RRID:SCR_026110) | software application, software resource, source code | Software tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps in high resolutions (10kbp all the way to 500bp and even more). Used to detect chromatin loops caused by interaction of DNA segments with variable size. | detect chromatin loops, interaction of DNA segments, Hi-C, Micro-C, contact maps, | NIGMS R35 GM128938 | PMID:32998764 | Free, Available for download, Freely available | SCR_026110 | Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation | 2026-09-12 01:04:57 | 6 | ||||||||
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cooltools Resource Report Resource Website 10+ mentions |
cooltools (RRID:SCR_026118) | software resource, software toolkit, source code | Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation. | enables reproducible analysis, high-resolution contact frequency data, paired python API, | NHGRI R01 HG003143; NHGRI UM1 HG011536; NIGMS R35 GM143116 |
PMID:38709825 | Free, Available for download, Freely available | SCR_026118 | 2026-09-12 01:04:58 | 42 | |||||||||
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LABRAT Resource Report Resource Website 1+ mentions |
LABRAT (RRID:SCR_025006) | software application, software resource, source code | Software application to quantify usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions. | quantify usage, alternative polyadenylation, cleavage sites, RNAseq data, identify genes, | NIGMS R35 GM118051; NIGMS R35 GM133885; NIGMS T32 GM008730; RNA Bioscience Initiative at the University of Colorado Anschutz Medical Campus |
DOI:10.1186/s12864-021-07781-1 | Free, Available for download, Freely available | SCR_025006 | Lightweight Alignment Based Resolution of Alternative Three prime ends | 2026-09-12 01:04:35 | 1 | ||||||||
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MAGeCK Resource Report Resource Website 100+ mentions |
MAGeCK (RRID:SCR_025016) | data analysis software, data processing software, software application, software resource | Software tool to identify important genes from genome-scale CRISPR-Cas9 screens. Used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. | identify genes, genome scale CRISPR-Cas9 screens, | Dana-Farber Cancer Institute ; NIGMS R01 GM099409 |
PMID:25476604 | Free, Available for download, Freely available | https://github.com/liulab-dfci/MAGeCK | SCR_025016 | Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout | 2026-09-12 01:04:36 | 232 | |||||||
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CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | data access protocol, data or information resource, database, software resource, web service | Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions. | Mass Spectrometry contaminants, standardized negative controls, contaminant repository, AP-MS analysis, affinity purification, mass spectrometry data, | Austrian Academy of Sciences ; Austrian Federal Ministry for Science and Research ; Austrian Science Fund ; Canadian Institutes of Health Research ; European Molecular Biology Organisation ; European Research Council ; European Union 7th Framework Program ; government of Ontario ; Human Frontier Science Program ; NCI R21 CA16006001A1; Netherlands Proteomics Center ; NHLBI HL112618-01; NIDA DP1DA026192; NIGMS 5R01GM94231; Stowers Institute for Medical Research |
PMID:23921808 | Free, Freely available, | https://reprint-apms.org/ | SCR_025008 | CRAPome:Contaminant Repository for Affinity Purification | 2026-09-12 01:04:35 | 24 | |||||||
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Cytoscape StringApp Resource Report Resource Website 10+ mentions |
Cytoscape StringApp (RRID:SCR_025009) | software application, software resource, source code | Software application for network analysis and visualization of proteomics data. Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains appearance and many of features of STRING, and integrates data from associated databases. | protein networks, network analysis and visualization, proteomics data, | is a plug in for: STRING | Chan Zuckerberg Initiative ; Danish Council for Independent Research ; NIGMS P41 GM103504; Novo Nordisk Foundation ; Silicon Valley Community Foundation |
PMID:30450911 | Free, Available for download, Freely available | https://github.com/RBVI/StringApp | SCR_025009 | stringApp | 2026-09-12 01:04:35 | 40 | ||||||
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ReDU Resource Report Resource Website 1+ mentions |
ReDU (RRID:SCR_025105) | data access protocol, software resource, web service | Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE. | Mass Spectrometry data, find uniformly formatted public MS/MS data, formatted metadata, Global Natural Product Social Molecular Networking Platform, GNPS, find and re-analyze public Mass Spectrometry data, ReDU metadata standards, data validator, | has parent organization: University of California at San Diego; California; USA | American Society for Mass Spectrometry ; FAPESP ; Gordon and Betty Moore Foundation ; Krupp Endowed Fund ; NCI R03 CA211211; Netherlands eScience Center ; NIGMS P41 GM103484; NIGMS R01 GM107550; NSF ; Sloan Foundation ; University of California ; San Diego Center for Microbiome Innovation SEED grants ; US Office of Naval Research |
PMID:32807955 | Free, Freely available | SCR_025105 | Reanalysis of Data User | 2026-09-12 01:04:37 | 2 | |||||||
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MassQL Resource Report Resource Website 1+ mentions |
MassQL (RRID:SCR_025106) | software resource, source code | Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data. | Mass Spectrometry data searching, mass spectrometry data, mining of MS data, common MS terminology, mass spectrometry patterns, raw data query, | AMED Japan Program for Infectious Diseases Research and Infrastructure ; Betty and Gordon Moore Foundation ; Burroughs Wellcome Fund ; Czech Science Foundation ; German Ministry for Education and Research ; German Research Foundation ; Horizon 2020 programme of the European Union ; Ministry of Innovative Development of the Republic of Uzbekistan ; National Cancer Center Research and Development Fund ; National Research Foundation of Korea ; NIAID R15 AI137996; NIAID R21 AI156669; NIGMS R01 GM107550; NIGMS R01 GM125943; NIGMS R35 GM128690; Novo Nordisk Foundation ; Denmark ; NSF ; Swedish Research Council ; U.S. Department of Energy Joint Genome Institute ; University of Michigan |
DOI:10.1101/2022.08.06.503000 | Free, Available for download, Freely available | https://pypi.org/project/massql/ | SCR_025106 | Mass Spec Query Language | 2026-09-12 01:04:37 | 1 | |||||||
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Find My Understudied Genes Resource Report Resource Website 1+ mentions |
Find My Understudied Genes (RRID:SCR_025047) | FMUG | software application, software resource, source code | Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors. Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms. | has parent organization: Northwestern University; Illinois; USA | Moderna Inc ; NAIAD U19AI135964; NIA K99AG068544; NIGMS T32GM008449; Northwestern University ; NSF ; Simons Foundation |
DOI:10.7554/eLife.93429 | Free, Available for download, Freely available | https://github.com/amarallab/fmug | SCR_025047 | 2026-09-12 01:04:36 | 3 | |||||||
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glmpca Resource Report Resource Website 1+ mentions |
glmpca (RRID:SCR_025517) | software resource, software toolkit, source code | Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data. | dimension reduction, non-normally distributed data, principal components analysis, | Chan-Zuckerberg Initiative ; NCI T32CA009337; NHGRI P41HG004059; NHGRI R00HG009007; NHGRI R01HG005220; NIGMS R01GM083084 |
PMID:31870412 | Free, Available for download, Freely available, | https://CRAN.R-project.org/package=glmpca | SCR_025517 | generalized version of principal components analysis | 2026-09-12 01:04:46 | 2 | |||||||
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WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | software resource, software toolkit, source code | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG006123; NHGRI HG007036; NIGMS GM007197; NIMH MH101825; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-09-12 01:04:45 | 3 | |||||||||
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mergem Resource Report Resource Website |
mergem (RRID:SCR_028616) | software resource, software toolkit | Software Python package and command-line tool for merging, comparing, and translating genome-scale metabolic models. | merging, comparing, translating, genome-scale metabolic models, | is organization facet of: University of Maryland; Maryland; USA | NIGMS R35GM137953 | PMID:38312936 | Free, Available for download, Freely available | https://zenodo.org/records/10740987 | SCR_028616 | 2026-09-12 01:05:55 | 0 | |||||||
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University of Kansas Nanofabrication Core Facility Resource Report Resource Website |
University of Kansas Nanofabrication Core Facility (RRID:SCR_028756) | access service resource, core facility, service resource | Provides manufacturing micro- and nanofluidic devices for biomedical research, equipment and resources for applications with micro- and nanofabrication needs. Facility conisists of ISO class 7 cleanroom space, housing tools and materials for techniques including photolithography, nano-imprint lithography, plasma (dry) etching (ICP-RIE), wet etching, thin film deposition, scanning electron microscopy (VP-SEM), atomic force microscopy, contact angle goniometry, ellipsometry, profilometry, wafer dicing, wire bonding, laser ablation and engraving, 3D printing, hot embossing, and COMSOL software for device modeling. In addition, the facility has numerous microscopes for general inspection, ovens and furnaces, ultrapure water, and dedicated process fume hoods. | ABRF, nanofabrication cleanroom facility, biomedical research device, device manufacturing, |
is listed by: ABRF CoreMarketplace has parent organization: University of Kansas; Kansas; USA |
NIGMS P30GM145499 | Restricted | ABRF_6056 | https://coremarketplace.org/?FacilityID=6056&citation=1 | SCR_028756 | University of Kansas Nanofabrication Facility (KUNF) | 2026-09-12 01:05:59 | 0 |
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