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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | ||||||||
|
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 | ||||||||
|
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 | ||||||||
|
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 | |||||||||
|
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 | |||||||||
|
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 | ||||||||
|
BioLiP Resource Report Resource Website 100+ mentions |
BioLiP (RRID:SCR_027685) | data or information resource, database | Semi-manually curated database for biologically relevant ligand-protein binding interactions. Structure data are collected primarily from Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. Database used for serving needs of ligand-protein docking, virtual ligand screening and protein function annotation.BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes, integrates structural alignment algorithms with structure prediction techniques, which enables composite protein structure and sequence-based searching. | curated database, ligand-protein binding interactions, ligand-protein docking, virtual ligand screening, protein function annotation, | uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) | National Science Foundation ; NIGMS GM083107; NIGMS GM084222 |
PMID:23087378 PMID:37522378 |
Free, Freely available | SCR_027685 | BioLiP2 | 2026-09-05 06:35:55 | 127 | |||||||
|
SQuIRE Resource Report Resource Website 10+ mentions |
SQuIRE (RRID:SCR_027719) | SQuIRE | software resource, software toolkit, source code | Software RNA-seq analysis pipeline that provides quantitative and locus-specific picture of Transposable Elements expression. | RNA-seq analysis, quantitative and locus-specific picture of TE expression, Transposable Elements expression, | NIGMS P50GM107632; NIGMS R01GM124531 |
PMID:30624635 | Free, Available for download, Freely available | SCR_027719 | , Software for Quantifying Interspersed Repeat Expression (SQuIRE), Software for Quantifying Interspersed Repeat Expression | 2026-09-05 06:35:56 | 11 | |||||||
|
BISCUIT Resource Report Resource Website 1+ mentions |
BISCUIT (RRID:SCR_028006) | software resource, software toolkit | Software application for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Used to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data. Analyzing sodium bisulfite conversion-based DNA methylation/modification data. | simultaneous genetic and epigenetic inference, analyzing sodium bisulfite conversion-based DNA methylation/modification data, perform alignment, DNA methylation, mutation calling, allele specific methylation, bisulfite sequencing data, | NCI R37CA230748; NCI U24CA264023; NIGMS R35GM146978 |
PMID:38412294 | Free, Available for download, Freely available | SCR_028006 | , BISulfite-seq CUI Toolkit, BISulfite-seq CUI Toolkit (BISCUIT) | 2026-09-05 06:36:04 | 2 | ||||||||
|
EpiProfile Resource Report Resource Website |
EpiProfile (RRID:SCR_028224) | software application, software resource, source code | Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis. | LC-MS/MS analysis, peptide, quantification, histone, quantification of histone peptides, quantification of histone peptides based on LC-MS/MS analysis, mass spectrometry data, | NCATS TL1TR001880; NCI CA196539; NIAID AI118891; NIGMS GM110174; NIGMS T32GM008275; UPenn Epigenetics Institute |
PMID:25805797 PMID:29790754 |
Free, Available for download, Freely available | SCR_028224 | EpiProfile 2.0 | 2026-09-05 06:36:08 | 0 | ||||||||
|
HiTAIC Resource Report Resource Website |
HiTAIC (RRID:SCR_028181) | data access protocol, software resource, web service | Web-based application to trace tumor tissue of origin in primary and metastasized cancers. | Tumor classifier, trace tumor tissue of origin, primary and metastasized cancers, | NCI P30CA023108; NCI R01CA216265; NCI R01CA253976; NCI R01CA275974; NIGMS P20GM104416 |
PMID:37089814 | Free, Freely available | SCR_028181 | Hierarchical Tumor Artificial Intelligence Classifier | 2026-09-05 06:36:07 | 0 | ||||||||
|
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 | 2026-09-05 06:36:16 | 0 | |||||||
|
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) | 2026-09-05 06:36:18 | 0 | ||||||
|
MARIA Resource Report Resource Website |
MARIA (RRID:SCR_028673) | software resource, web application | Web multimodal recurrent neural network tool designed to predict HLA-II (Human Leukocyte Antigen class II) peptide ligand presentation. It uses cell HLA alleles, peptide sequences, and source genes to evaluate antigen presentation. Used for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. | multimodal recurrent neural network, predicting likelihood of antigen presentation, gene of interest, specific HLA class II alleles, | is organization facet of: Stanford University; Stanford; California | NCI K08 CA207882; NCI U01 CA194389; NCRR S10RR027431; NIGMS GM 102365 |
PMID:31611695 | Free, Freely available | SCR_028673 | MARIA:Major Histocompatibility Complex Analysis with Recurrent Integrated Architecture | 2026-09-05 06:36:17 | 0 | |||||||
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University of Arkansas AIMRC Data Science Core Facility Resource Report Resource Website |
University of Arkansas AIMRC Data Science Core Facility (RRID:SCR_028681) | access service resource, core facility, service resource | Core specializes in artificial intelligence-based approaches to elucidate relationships between large imaging, bioenergetics, genomic, and proteomic data sets. Provided services include: 1) foundational training for those getting started with high-performance computing and Arkansas Research Platform (ARP), 2) training and support for the collaborative use of a 508 TB data storage server exclusively maintained for and catering to AIMRC researchers, 3) training for Python programming, basic data mining, and machine learning, 4) training and support for using open-source deep learning based biomedical imaging resources (e.g., ZeroCostDL4Mic and Bioimage Model Zoo), and 5) customized solutions for deep learning based and large foundational models based biomedical imaging analysis, multi-omics data integration and analysis, and quantitative analysis pipelines for large data sets. | ABRF, Center of Biomedical Research Excellence (COBRE), data science services, large imaging, bioenergetics, genomic, proteomic, data sets, |
is listed by: ABRF CoreMarketplace has parent organization: University of Arkansas; Arkansas; USA |
NIGMS P20GM139768 | ABRF_6033 | https://coremarketplace.org/RRID:SCR_028681/?citation=1 | SCR_028681 | , Arkansas Integrative Metabolic Center (AIMRC) Data Science Core | 2026-09-05 06:36:17 | 0 | |||||||
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Creighton University Flow Cytometry Core Facility Resource Report Resource Website |
Creighton University Flow Cytometry Core Facility (RRID:SCR_028881) | access service resource, core facility, service resource | Core provides flow cytometry services. | ABRF, flow cytometry services, |
is listed by: ABRF CoreMarketplace has parent organization: Creighton University; Nebraska; USA |
NIGMS 3P20GM139762; NIGMS 3R01GM102487 |
Restricted | ABRF_6145 | https://coremarketplace.org/?FacilityID=6145&citation=1 | SCR_028881 | CU Flow Cytometry Core | 2026-09-05 06:36:21 | 0 | ||||||
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Ocean State Research Institute Providence VA Medical Center Cell Isolation and Organ Function Core Facility Resource Report Resource Website |
Ocean State Research Institute Providence VA Medical Center Cell Isolation and Organ Function Core Facility (RRID:SCR_028797) | CIOF Core | access service resource, core facility, service resource | Core provides investigators with access to specialized expertise in primary cell isolation, ex vivo organ function assessment, histology, and advanced tissue imaging. The Core supports cardiovascular, pulmonary, and vascular research through customized experimental services, consultation, and rigorous functional and molecular analyses that accelerate mechanistic discovery and translational research. | ABRF, Primary Cell Isolation, Endothelial Cell Biology, Cardiac Fibroblasts, Ex Vivo Organ Function, Vascular Function, Histology, Immunohistochemistry, Immunofluorescence, RNAscope, Quantitative Image Analysis, Tissue Phenotyping, Cardiovascular Biology, Pulmonary Biology, Translational Research | is listed by: ABRF CoreMarketplace | NIGMS P30GM149398 | ABRF_6114 | https://coremarketplace.org/RRID:SCR_028797/?citation=1 | SCR_028797 | , Cell Isolation and Organ Function (CIOF) Core | 2026-09-05 06:36:19 | 0 |
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