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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PhenoMeNal Resource Report Resource Website 1+ mentions |
PhenoMeNal (RRID:SCR_016605) | phnmnl, PhenoMeNal | organization portal, portal, software resource, data access protocol, web service, consortium, data or information resource | Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics. | metabolomic, phenomic, data, processing, analysis, information, mining. medical, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory has parent organization: European Bioinformatics Institute |
European Commission EC654241 | Free, Registration required, Tutorial available | biotools:PhenoMeNal | https://github.com/phnmnl https://bio.tools/PhenoMeNal |
SCR_016605 | Phenome and Metabolome aNalysis | 2026-02-15 09:21:53 | 2 | |||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | software application, data visualization software, data processing software, software resource, data analysis software | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-02-15 09:21:45 | 66 | ||||
|
National Sleep Research Resource (NSRR) Resource Report Resource Website 50+ mentions |
National Sleep Research Resource (NSRR) (RRID:SCR_016576) | NSRR | organization portal, data or information resource, portal | System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community. | sleep, clinical, data, cohort, study, trial, dataset, visualization, exploration |
is recommended by: National Library of Medicine lists: Apnea, Bariatric surgery, and CPAP study lists: Sleep Heart Health Study lists: Honolulu-Asia Aging Study of Sleep Apnea lists: Cleveland Family Study lists: Cleveland Children's Sleep and Health Study lists: Best Apnea Interventions for Research (BestAIR) sleep study |
sleep apnea | NHLBI | PMID:29860441 | Free, Freely available, Registration required for membership | https://sleepdata.org/share https://sleepdata.org/datasets |
SCR_016576 | National Sleep Research Resource | 2026-02-15 09:21:53 | 68 | ||||
|
eulerAPE Resource Report Resource Website 10+ mentions |
eulerAPE (RRID:SCR_016457) | software application, data visualization software, data processing software, software resource | Software that uses ellipses to automatically draw accurate area-proportional Venn diagrams for 3-set data. It generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region. | euler, venn, diagram, graph, mathematics, math, data, draw | School of Computing ; University of Kent ; UK |
PMID:25032825 | SCR_016457 | Euler Ape | 2026-02-15 09:21:41 | 31 | |||||||||
|
Assemblosis Resource Report Resource Website 1+ mentions |
Assemblosis (RRID:SCR_016571) | software application, data processing software, software resource, training material, data or information resource, narrative resource, workflow | Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads. | common, workflow, language, automated, assemble, haploid, diploid, eukaryote, genome, longread, shortread, data | Free, Available for download, Freely available | SCR_016571 | 2026-02-15 09:21:43 | 1 | |||||||||||
|
NetCirChro Resource Report Resource Website |
NetCirChro (RRID:SCR_016616) | NetCirChro | software application, data visualization software, data processing software, software resource, data analysis software | Software interactive tool for visualizing and analyzing network data in the spatial context of the chromosome. Used to discover the role of gene organization in functional regulatory networks. Plugin enables users of Cytoscape to overlay networks onto a circular chromosomal map. | visualization, analyzing, network, data, gene, spatial, chromosome, circular, map |
is listed by: NIDDK Information Network (dkNET) has parent organization: NIAID works with: Cytoscape |
Free, Available for download, Freely available | SCR_016616 | Networks on Circular Chromosome | 2026-02-15 09:21:09 | 0 | ||||||||
|
Honolulu-Asia Aging Study of Sleep Apnea Resource Report Resource Website |
Honolulu-Asia Aging Study of Sleep Apnea (RRID:SCR_016587) | HAASSA | disease-related portal, topical portal, data or information resource, portal | Portal for sleep-disordered breathing (SDB) in an elderly cohort of Japanese-American men under surveillance for Alzheimer disease (AD) and other dementias. Data to assess relationships between SDB and cognitive performance in late life. | data, polysomnography, aging, sleep, disordered, breathing, elderly, Japanese-American, men, Alzheimer | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | PMID:12938814 | Permission required | SCR_016587 | Honolulu Asia Aging Study of Sleep Apnea | 2026-02-15 09:21:53 | 0 | ||||||
|
Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | disease-related portal, topical portal, data or information resource, portal | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380; NCRR M01 RR00080 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-02-15 09:21:44 | 3 | ||||||
|
dplyr Resource Report Resource Website 100+ mentions |
dplyr (RRID:SCR_016708) | software application, data processing software, data analysis software, software resource | Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange. | data, frame, object, in and of memory, grammar, manipulation, set, verb, mutate, select, filter, summerise, arrange |
is used by: PlotsOfData is used by: tidyverse is listed by: CRAN is related to: R Project for Statistical Computing works with: tidyr |
Open Source, Available for download | https://github.com/tidyverse/dplyr https://dplyr.tidyverse.org/ |
SCR_016708 | 2026-02-15 09:21:54 | 200 | |||||||||
|
MAJIQ Resource Report Resource Website 10+ mentions |
MAJIQ (RRID:SCR_016706) | MAJIQ, | software application, data processing software, software resource, software toolkit, data analysis software | Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis. | detect, quantify, local, splicing, variation, RNA-Seq, data, replicate, differential, analysis | has parent organization: University of Pennsylvania; Philadelphia; USA | NIA R01 AG046544; Penn Institute for Biomedical Informatics Pilot |
PMID:29236961 | Free, Available for download, Freely available, Tutorial available | SCR_016706 | MAJIQ, MAJIQ/Viola, Modeling Alternative Junction Inclusion Quantification | 2026-02-15 09:21:47 | 30 | ||||||
|
Open Data Commons for Spinal Cord Injury Resource Report Resource Website 10+ mentions |
Open Data Commons for Spinal Cord Injury (RRID:SCR_016673) | odc-sci, ODC-SCI | portal, service resource, storage service resource, data repository, data or information resource, topical portal | Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research. | spinal, cord, injury, data, repository |
is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
Craig H. Neilsen Foundation | Free, Registration required | r3d100014071 | https://doi.org/10.34945/ https://dx.doi.org/10.34945/ https://api.datacite.org/dois?prefix=10.34945 https://doi.org/10.17616/R31NJNCN |
SCR_016673 | , Open Data Commons for Spinal Cord Injury, Open Data Commons at UCSD FDI Lab | 2026-02-15 09:21:54 | 40 | |||||
|
Colour maps for brain imaging Resource Report Resource Website 1+ mentions |
Colour maps for brain imaging (RRID:SCR_016715) | software application, data visualization software, data processing software, software resource, image analysis software | Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging. | perceptually, uniform, color, map, brain, data, imaging |
is related to: MRIcron is related to: MATLAB has parent organization: University of Western Australia; Perth; Australia |
Free, Available for download, Freely available | SCR_016715 | Colour maps, brain_colours, colour maps, brain colours, Brain colours, colour maps for brain imaging, Colour maps for brain imaging | 2026-02-15 09:21:10 | 1 | |||||||||
|
ANOCVA Resource Report Resource Website |
ANOCVA (RRID:SCR_016719) | ANOCVA | software application, data processing software, data analysis software, software resource | Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders. | nonparametric, statistical, test, compare, clustering, structure, functional, brain, network, magnetic, resonance, imaging, data, fMRI, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: CRAN |
CAPES and CNPq Fellowships ; State of São Paulo Research Foundation ; Pew Latin American Fellowship ; Ciência sem Fronteiras Fellowship ; NAP eScience |
PMID:28174516 | Free, Available for download, Freely available | biotools:anocva | https://bio.tools/anocva | SCR_016719 | ANalysis Of Cluster VAriability, Analysis of Cluster Variability | 2026-02-15 09:21:47 | 0 | ||||
|
MetaboAnalystR Resource Report Resource Website 100+ mentions |
MetaboAnalystR (RRID:SCR_016723) | software application, data visualization software, data processing software, software resource, data analysis software | Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation. | analysis, metabolomic, data, analysis, vixualization, functional, interpretation | works with: MetaboAnalyst | Natural Sciences and Engineering Research Council of Canada ; Canada Research Chairs ; McGill Graduate Dean Award |
PMID:29955821 | Free, Available for download, Freely available | SCR_016723 | 2026-02-15 09:21:47 | 410 | ||||||||
|
OptiQuant Software Resource Report Resource Website 1+ mentions |
OptiQuant Software (RRID:SCR_016769) | software application, data processing software, software resource, data acquisition software, image analysis software, image acquisition software, data analysis software | Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer. | image, acquisition, analysis, display, archiving, quantify, autoradiography, data, PerkinElmer | Commercially available, Free download available | https://optiquant.software.informer.com/5.0/ | SCR_016769 | OptiQuant, OptiQuant 3.0, OptiQuant software 5.0, OptiQuant 5.0 | 2026-02-15 09:21:55 | 4 | |||||||||
|
BISE Resource Report Resource Website 10+ mentions |
BISE (RRID:SCR_016774) | organization portal, portal, database, software resource, service resource, production service resource, data or information resource, analysis service resource | Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows. | bioimage, analysis, data, information, image, processing, algorithm, workflow, bio.tools |
lists: FibrilTool is listed by: Debian is listed by: bio.tools has parent organization: NEUBIAS |
Free, Freely available, Registration required | biotools:BISE | https://bio.tools/BISE | SCR_016774 | 2026-02-15 09:21:48 | 12 | ||||||||
|
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS Resource Report Resource Website 500+ mentions |
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) | software application, data processing software, software resource, data analytics software, data acquisition software, software toolkit, data analysis software | Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise. | compound, centric, data, mining, navigation, chromatic, separation, coeluting, peak, signal, noise, mass, spectrometry, analysis, qualitative |
is listed by: OMICtools is related to: Agilent Masshunter Quantitative Analysis software has parent organization: Agilent Technologies |
SCR_016657 | 2026-02-15 09:21:54 | 733 | |||||||||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-02-15 09:21:09 | 5 | ||||
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IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | software application, sequence analysis software, data processing software, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer. | next, generation, analysis, genomic, data, cancer, genome |
is listed by: Debian has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/broadinstitute/gatk/ https://sources.debian.org/src/gatk/ |
SCR_016663 | GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper | 2026-02-15 09:21:09 | 63 | |||||||
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Sequenza Resource Report Resource Website 50+ mentions |
Sequenza (RRID:SCR_016662) | software application, data visualization software, data processing software, software resource, data analysis software | Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization. | estimate, copy, number, tumor, genome, sequencing, data, cellularity, ploidy, alteration, cancer, mutation, detection, quantification, visualization |
is listed by: CRAN has parent organization: Technical University of Denmark; Lyngby; Denmark |
European Commission 7th Framework Programme ; Danish Council for Independent Research ; Breast Cancer Research Foundation |
PMID:25319062 | https://cran.r-project.org/web/packages/sequenza/ | SCR_016662 | 2026-02-15 09:21:54 | 54 |
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