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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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circular statistics Resource Report Resource Website 10+ mentions |
circular statistics (RRID:SCR_016651) | CircStat | data analysis software, software resource, data processing software, software application | Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data. | circular, inferential, statistics, directional, data |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany works with: MATLAB |
German National Academic Foundation ; German Ministry of Education ; Science ; Research and Technology |
DOI:10.18637/jss.v031.i10 | Free, Available for download, Registration required to MathWorks Account, | https://github.com/circstat/circstat-matlab | SCR_016651 | Matlab Circular Statistics Toolbox, , circstat-matlab, circular statistics, Circular Statistics, CircStat for Matlab | 2026-02-14 02:03:15 | 42 | |||||
|
XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. | correct, technical, bias, sex, chromosome, next, generation, sequencing, data | is listed by: OMICtools | NIGMS R35 GM124827 | DOI:10.1101/346940 | Free, Available for download, Freely available | SCR_016661 | 2026-02-14 02:03:05 | 1 | ||||||||
|
LoomPy Resource Report Resource Website 10+ mentions |
LoomPy (RRID:SCR_016666) | LoomPy | software resource, data processing software, software application, data storage software | Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Created in HDF5 file format and can be opened from programming languages, including Python, R, C, C++, Java, MATLAB, Mathematica, and Julia. | Python, Loom, file, format, store, organize, omics, dataset, single, cell, expression, data, HDF5 |
is used by: BICCN works with: loom-viewer |
Free, Available for download, Freely available | https://linnarssonlab.org/loompy/ https://github.com/linnarsson-lab/loompy |
SCR_016666 | Loompy v2.0, Loompy v2.0.14, Loom Python, LoomPy, LoomPython | 2026-02-14 02:03:05 | 34 | |||||||
|
Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge https://bio.tools/centrifuge https://sources.debian.org/src/centrifuge/ |
SCR_016665 | 2026-02-14 02:03:18 | 9 | ||||||
|
PaVE Resource Report Resource Website 100+ mentions |
PaVE (RRID:SCR_016599) | PaVE | web application, data analysis service, analysis service resource, data or information resource, production service resource, service resource, software resource, database | Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information. | data, curated, papilloma, virus, genomic, sequence, analysis, storage, annotation, FASEB list | is listed by: NIAID | NIAID ZIA AI001071 | PMID:28053164 | Open source | SCR_016599 | PapillomaVirus Episteme, Papillomavirus Episteme | 2026-02-14 02:03:07 | 125 | ||||||
|
TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | data repository, storage service resource, portal, consortium, data or information resource, organization portal, service resource, disease-related portal, topical portal | Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data. | collect, data, sharing, analysis, tuberculosis, global, bio.tools |
is listed by: NIAID is listed by: bio.tools is listed by: Debian |
tuberculosis | NIH | DOI:10.1128/JCM.01013-17 | Free, Freely available | r3d100013925, biotools:TB_Portals | https://bio.tools/TB_Portals https://doi.org/10.17616/R31NJN8L |
SCR_016594 | 2026-02-14 02:03:17 | 12 | |||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | software resource, data visualization software, data processing software, software application | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow https://bio.tools/nmrprocflow https://github.com/inra/nmrprocflow |
SCR_016592 | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-02-14 02:03:07 | 23 | |||||
|
Open Reading Frame Finder Resource Report Resource Website 1000+ mentions |
Open Reading Frame Finder (RRID:SCR_016643) | ORF finder | sequence analysis software, data processing software, analysis service resource, data analysis software, production service resource, service resource, software application, software resource | Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long. | search, open, reading, frame, DNA, sequence, ORF, protein, translation, data, encoding, segment, verify |
uses: BLASTP has parent organization: NCBI |
Free, Available for download, Freely available | SCR_016643 | Open Reading Frame finder, Open Reading Frame Finder | 2026-02-14 02:03:18 | 1428 | ||||||||
|
Walter Reed Biosystematics Unit Resource Report Resource Website 1+ mentions |
Walter Reed Biosystematics Unit (RRID:SCR_016729) | WRBU | data or information resource, organism-related portal, portal, topical portal | National resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections. | medically, important, arthropods, maintanace, repository, U.S. mosquito, data, vector, collection | is parent organization of: VectorMap | SCR_016729 | The Walter Reed Biosystematics Unit, WRBU, Walter Reed Biosystematics Unit | 2026-02-14 02:03:16 | 5 | |||||||||
|
RnaSeqGeneEdgeRQL Resource Report Resource Website |
RnaSeqGeneEdgeRQL (RRID:SCR_016699) | data processing software, data analysis software, software toolkit, software application, software resource | Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment. | study, analysis, RNA, sequencing, read, alignment, data | is affiliated with: Bioconductor | Free, Available for download, Freely available | SCR_016699 | 2026-02-14 02:03:08 | 0 | ||||||||||
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HASP Resource Report Resource Website |
HASP (RRID:SCR_016615) | HASP | data visualization software, data processing software, data or information resource, software application, software resource, database | Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. | structural, visualization, phylogenetic, biochemical, immunological, hemagglutinin, data, 3D, |
is listed by: NIAID is listed by: NIDDK Information Network (dkNET) |
NIAID | DOI:10.1186/1471-2105-14-197 | Free, Freely available | SCR_016615 | HemAgglutinin Structure Prediction, Hemagglutinin Structure Prediction | 2026-02-14 02:03:15 | 0 | ||||||
|
Cleveland Children's Sleep and Health Study Resource Report Resource Website |
Cleveland Children's Sleep and Health Study (RRID:SCR_016584) | CCSHS | disease-related portal, data or information resource, portal, topical portal | Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR. | data, pediatric, cohort, sleep, study, EEG, ECG, EOG, EMG, SpO2, polysomnography | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | PMID:12712055 PMID:16335483 DOI:10.1080/15402002.2013.825838 |
SCR_016584 | Cleveland Children's Sleep and Health Study | 2026-02-14 02:03:04 | 0 | |||||||
|
Best Apnea Interventions for Research (BestAIR) sleep study Resource Report Resource Website 1+ mentions |
Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) | BestAIR | disease-related portal, data or information resource, portal, topical portal | Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume. | data, analysis, sleep, apnea, treatment, cardiovascular, disease, risk, factor, polysomnography, ECG, SpO2 | is listed by: National Sleep Research Resource (NSRR) | sleep apnea, cardiovascular disease | ResMed Foundation ; Philips Respironics ; NHLBI U34 HL105277 |
DOI:10.5665/sleep.4266 | SCR_016583 | bestair, , Best Apnea Interventions for Research, Bestair | 2026-02-14 02:03:17 | 2 | ||||||
|
Washington University School of Medicine Knight ADRC Request Center Resources Core Facility Resource Report Resource Website 1+ mentions |
Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) | core facility, access service resource, service resource | Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources. | ABRF, Alzheimer research, Data, OASIS, Biospecimen, tissue, imaging, |
is listed by: ABRF CoreMarketplace has parent organization: Washington University School of Medicine Knight Alzheimers Disease Research Center has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Alzheimer disease, dementia | NIA P30AG066444; NIA P01AG026276; NIA U19 AG0032438; NIA P01AG003991 |
ABRF_2734 | https://coremarketplace.org/?FacilityID=2734&citation=1 | SCR_025254 | ADRC Request Center Resources | 2026-02-14 02:08:42 | 2 | ||||||
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DSigDB Resource Report Resource Website 50+ mentions |
DSigDB (RRID:SCR_026202) | data or information resource, database | Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets. | gene sets, quantitative inhibition, drug induced, gene expression changes, data, drugs, compounds, | NCI P30CA046934; NCI P50CA058187 |
PMID:25990557 | Free, Freely available, | SCR_026202 | , Drug Signatures Database, drug SIGnatures DataBase | 2026-02-14 02:08:58 | 82 | ||||||||
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MarmotGraph Resource Report Resource Website |
MarmotGraph (RRID:SCR_027452) | software resource, software application, knowledge graph | Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs. | Metadata, managing, system, neuroscience, experimental, data, human, brain, graph, database, terminology, ontology | is related to: EBRAINS Knowledge Graph | Free, Freely available, | SCR_027452 | Management Applications for Rich Metadata ObjecTs Graph | 2026-02-14 02:09:31 | 0 | |||||||||
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Concept Hub Resource Report Resource Website |
Concept Hub (RRID:SCR_013586) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. A database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub. | collaboration, concept, consumer, data, developer, health care, terminology | is related to: HDD Access | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. | SCR_013586 | ConceptHub | 2026-02-14 02:10:05 | 0 | |||||||||
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Brigham and Women’s Hospital NeuroTechnology Studio Core Facility Resource Report Resource Website |
Brigham and Women’s Hospital NeuroTechnology Studio Core Facility (RRID:SCR_027687) | core facility, access service resource, service resource | Offers advanced instrumentation and expert support to advance understanding of brain function and brain disease by providing researchers with access to cutting-edge technologies. Provides access to advanced instrumentation for optical microscopy, genomics, metabolic imaging and other technologies, as well as image analysis software. Provides expert support and training, data quality and interpretation. | ABRF, optical microscopy, genomics, metabolics, imaging, training, data, neuroscience, image analysis, |
is listed by: ABRF CoreMarketplace has parent organization: Harvard Medical School; Massachusetts; USA |
Restricted | ABRF_5659 | https://coremarketplace.org/RRID:SCR_027687/?citation=1 | SCR_027687 | 2026-02-14 02:10:07 | 0 | ||||||||
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BIDMC Division of Digital Psychiatry LAMP platform Core Facility Resource Report Resource Website |
BIDMC Division of Digital Psychiatry LAMP platform Core Facility (RRID:SCR_027767) | data or information resource, core facility, service resource, access service resource | Core collects data to capture and consider the real-time lived experiences of patients. Uses open-source digital platform and mobile app for neuropsychiatric research and clinical care, to monitor, support, and improve brain health by collecting real-time data (like location, activity, heart rate via sensors), conducting digital assessments (surveys, cognitive tests), and delivering interventions (meditation, journaling, psychoeducation) to patients and clinicians. It helps study behavioral patterns, track symptoms, and personalize mental health treatment through features organized around Learn, Assess, Manage, and Prevent. | ABRF, study behavioral patterns, track symptoms, personalize mental health treatment, data, neuropsychiatric research and clinical care management platform, run remote smartphone-based research studies, |
is listed by: ABRF CoreMarketplace has parent organization: Harvard Medical School; Massachusetts; USA |
ABRF_3107 | https://coremarketplace.org/?FacilityID=3107 https://docs.lamp.digital/ https://github.com/BIDMCDigitalPsychiatry/LAMP-platform/ |
SCR_027767 | mindLAMP, BIDMC mindLAMP, Beth Israel Deaconess Medical Center mindLAMP | 2026-02-14 02:09:59 | 0 | ||||||||
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Collection of Alternative Methods for Regulatory Application (CAMERA) Resource Report Resource Website |
Collection of Alternative Methods for Regulatory Application (CAMERA) (RRID:SCR_027893) | CAMERA | data or information resource, database | Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance. | NAMSD, validated alternative methods, U.S. regulatory, validation study reports, data, protocols, SOPs, regulatory guidance, | Free, Freely available | SCR_027893 | Collection of Alternative Methods for Regulatory Application | 2026-02-14 02:09:33 | 0 |
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