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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-09-05 06:34:50 | 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 | 2026-09-05 06:34:48 | 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 | 2026-09-05 06:35:00 | 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 | 2026-09-05 06:35:00 | 3 | |||||||||
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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 | 2026-09-05 06:34:41 | 2 | ||||||||
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West Virginia University Flow Cytometry and Single Cell Core Facility Resource Report Resource Website 10+ mentions |
West Virginia University Flow Cytometry and Single Cell Core Facility (RRID:SCR_017738) | access service resource, core facility, service resource | Facility provides instrumentation and scientific support for single cell analysis and sorting. Routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell proliferation, cytokine production, and cell sorting based on expression of cell surface antigen(s) and/or expression of genetically engineered intercellular fluorescent proteins. | Single, cell, analysis, sorting, flow, cytometry, West Virginia, service, core | NCRR RR020866; NIGMS P20 GM103434; NIGMS P20 GM109098; NIGMS P30 GM103488; NIGMS U51 GM104942; NIGMS U54 GM104942; NIH Office of the Director S10 OD016165 |
Open | ABRF_221 | SCR_017738 | FCSCCF, WVU Flow Cytometry and Single Cell Core Facility | 2026-09-05 06:34:11 | 15 | ||||||||
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Arkansas University College of Medicine Flow Cytometry Core Facility Resource Report Resource Website |
Arkansas University College of Medicine Flow Cytometry Core Facility (RRID:SCR_017741) | access service resource, core facility, service resource | Core provides flow cytometry instrumentation and analysis. Instruments include Fortessa, FacsAria and Image Stream. | Flow, cytometry, biopolymer, proteomics, data, analysis, service, core | NIGMS P20 GM103625 | ABRF_215 | SCR_017741 | Biopolymers and Proteomics Core Facility | 2026-09-05 06:34:11 | 0 | |||||||||
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South Dakota University SD BRIN Proteomics Core Facility Resource Report Resource Website |
South Dakota University SD BRIN Proteomics Core Facility (RRID:SCR_017743) | access service resource, core facility, service resource | Core provides proteomics services to researchers from South Dakota and the surrounding region to rapidly analyze and identify protein expression patterns in their experimental systems.Develops experimental design, protocols, data analysis and interpretation.Provides consulting and advice in grant proposal, as well as data preparation to be submitted to proteomics journal according to requirements.Offers training in use of common equipment such as scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation. | Proteomics, protein, expression, analysis, data, experimental, design, training, service, core | NIGMS ; Sanford School of Medicine and South Dakota Biomedical Research Infrastructure Network |
Open | ABRF_224 | SCR_017743 | Proteomics Core | 2026-09-05 06:34:11 | 0 | ||||||||
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Brown University Transgenic and Gene Targeting Core Facility Resource Report Resource Website |
Brown University Transgenic and Gene Targeting Core Facility (RRID:SCR_017690) | MTGTF | access service resource, core facility, service resource | MTGTF is to support the investigators in using genetically modified mouse models in Brown University, affiliated hospitals and academic institutions in Rhode Island and other states. Provides services of molecular design and generation of transgenic and knock-out mouse models as well as general advice on use and management of such models. Conventional ES cell gene-targeting system is employed to serve as alternative or to fill the limitations of CRISPR/Cas9 system. Routine services include genotype analysis, sperm or embryo cryopreservation and storage, rederivation, in vitro fertilization (IVF). Other services, such as mouse vasectomy, embryo transfer, colony scale-up, intracytoplasmic sperm injection (ICSI) are also available. New services requiring MTGTF resources can be created through request. | Genetically, modified, mouse, model, support, molecular, design, transgenic, knock-out, ES, cell, targeting, system, CRISPR/Cas9, genotype, analysis, sperm, embryo, cryopreservation, storage, fertilization, vasectomy, service, core | NIGMS P30 GM103410 | Open | ABRF_79, SCR_017708 | SCR_017690 | Mouse Transgenic and Gene Targeting Facility | 2026-09-05 06:34:10 | 0 | |||||||
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Kansas University at Lawrence High Throughput Screening Laboratory Core Facility Resource Report Resource Website 1+ mentions |
Kansas University at Lawrence High Throughput Screening Laboratory Core Facility (RRID:SCR_017752) | KU-HTSL | access service resource, core facility, service resource | Core offers high throughput screening of large chemical libraries of compounds to identify novel chemical entities that target biological system of interest.Provides target identification and validation, assay development, high throughput screening, hit confirmation, data mining and medicinal chemistry to facilitate hit to lead development. | Screening, large, chemical, library, compound, novel, entity, target, identification, validation, assay, development, data, mining, medicinal, chemistry, service, core | NIGMS P30 GM103495; State of Kansas ; University of Kansas |
Open | ABRF_254 | SCR_017752 | High Throughput Screening Laboratory at KU | 2026-09-05 06:34:11 | 1 | |||||||
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University of New England In Vivo Behavior Core Facility Resource Report Resource Website 1+ mentions |
University of New England In Vivo Behavior Core Facility (RRID:SCR_017883) | access service resource, core facility, service resource | Core provides technical expertise, training, instrumentation and related services for assessing behavior in animals to help to gain insight into function of nervous system and mechanisms of acute and chronic pain. Services include Behavioral Testing; General Behavioral Phenotyping: Observational Screens, Motor Function; Pain/Sensory Testing: Thermal, Mechanical, Chemical; Additional Neurobehavioral Tests: Psychiatric, Addiction, Learning and Memory;Miscellaneous Systems: GI Transit, Cardiovascular and Respiration. Other Services: Assistance choosing behavioral test and statistical tests for assessing results; Training in surgical techniques for small animal surgeries; Staff expertise includes surgical methods for producing pain models; dosing of drugs/anesthetics including central, systemic and localized administration; and tissue extractions. | in vivo, behavior, pain, sensory testing, training, function, addiction, neuropathic, CIPN, , system, acute, chronic, mechanism, motor, learning, memory, neurobehavioral |
is listed by: ABRF CoreMarketplace has parent organization: University of New England; Biddeford; USA |
NIGMS P30GM145497 | Open | https://coremarketplace.org/?FacilityID=758 | SCR_017883 | In Vivo Behavior Core | 2026-09-05 06:34:14 | 1 | |||||||
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Nemours/A.I.duPont Hospital for Children Cell Science Core Facility Resource Report Resource Website |
Nemours/A.I.duPont Hospital for Children Cell Science Core Facility (RRID:SCR_017854) | CSC | access service resource, core facility, service resource | Core specializes in cell, protein, and small molecules analysis as well as cell culture techniques. Services include:2-D gel electrophoresis, 2-D DIGE, LC-MS/MS, HPLC, flow cytometry, fluorescence-activated cell sorting (FACS), cell and tissue culture, and immortalization of cell lines. Our staff works closely with investigators to help design, perform, and analyze experiments.Offers training and assistance in flow cytometry, tissue culture, and operation many of our walk-up instruments.Instruments:Cell Sorter: FACS Aria III, BD Biosciences;Flow Cytometers, analyzers:C6, Accuri/BD Biosciences;Novocyte 3000, ACEA Biosciences;software for analysis: FSC Express, DeNovo software;LC-MS/MS: 6460 Triple Quadrupole, Agilent;Typhoon Trio Scanner, GE Lifesciences;Blood Analyzer: Hemavet 950, Drew Scientific.Plate Readers:;Victor Nivo 5F, Perkin Elmer;Luminometer: Centro XS, Berthold.Services:Cell Sorting (FACS);2-D gel electrophoresis/2D-DIGE;LC-MS/MS analysis of compounds; Cell immortilization. | Cell, protein, small, molecules, analysis, culture, electrophoresis, 2D DIGE, LC-MS/MS, HPLC, FACS, immortalization, flow, cytometry, sorting, training, service, core, | NIGMS P30 GM114736 | Open | ABRF_662 | SCR_017854 | Cell Science Core | 2026-09-05 06:34:14 | 0 | |||||||
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scvi-tools Resource Report Resource Website 50+ mentions |
scvi-tools (RRID:SCR_026673) | data analysis software, data processing software, software application, software library, software resource, software toolkit, source code | Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData. | probabilistic analysis, single-cell omics data, spatial omics data, | Chan-Zuckerberg Foundation ; NHGRI T32HG000047; NIGMS R35GM124916 |
PMID:35132262 | Free, Available for download, Freely available | https://github.com/scverse/scvi-tools | SCR_026673 | single-cell variational inference tools | 2026-09-05 06:35:28 | 58 | |||||||
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ped-sim Resource Report Resource Website 1+ mentions |
ped-sim (RRID:SCR_026957) | simulation software, software application, software resource, source code | Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances. | Pedigree simulator, simulate pedigree structures, simulating relatives, sex-specific, sex averaged, genetic maps, | Alfred P. Sloan Research Fellowship ; NHLBI P01 HL045222; NHLBI R01 HL0113323; NIDDK R01 DK047482; NIDDK R01 DK053889; NIGMS R35 GM133805; NIGMS T32 GM007617; NIGMS T32 GM083937; United States-Israel Binational Science Foundation ; Wellcome Trust |
PMID:31860654 | Free, Available for download, Freely available | SCR_026957 | Ped-sim | 2026-09-05 06:35:35 | 4 | ||||||||
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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 | 2026-09-05 06:35:03 | 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 | 2026-09-05 06:35:06 | 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 | 2026-09-05 06:35:11 | 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 | 2026-09-05 06:35:13 | 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 | 2026-09-05 06:35:13 | 42 | |||||||||
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University of Nebraska Medical Center Animal Behavior Core Facility Resource Report Resource Website 1+ mentions |
University of Nebraska Medical Center Animal Behavior Core Facility (RRID:SCR_018830) | access service resource, core facility, service resource | Provides investigators with expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with focus on rigor, reproducibility, and maintaining the highest standards of animal welfare. | USEDit, acoustic, behavioral, cognitive, expertise, equipment, space service, ABRF, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Nebraska; Nebraska; USA |
NIGMS 1P20GM130447 | Restricted | ABRF_1021 | https://coremarketplace.org/?FacilityID=1021 | SCR_018830 | UNMC Animal Behavior Core, University of Nebraska Medical Center UNMC Animal Behavior Core, Animal Behavior Core | 2026-09-05 06:34:17 | 7 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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