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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ANOCVA Resource Report Resource Website |
ANOCVA (RRID:SCR_016719) | ANOCVA | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:43:58 | 0 | ||||
|
CARD Resource Report Resource Website 10+ mentions |
CARD (RRID:SCR_016602) | CARD | data analysis service, analysis service resource, software resource, production service resource, service resource, web application, database, data or information resource | Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data. | integrated, analysis, interactive, visualization, RNA, interfernce, screening, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Australian Cancer Research Foundation ; Victorian Department of Industry ; Innovation and Regional Development ; Australian Government’s Education Investment Fund ; Australasian Genomics Technologies Association ; Brockhoff Foundation ; Peter MacCallum Cancer Centre Foundation |
PMID:26902267 | Free, Freely available | biotools:CARD | https://bio.tools/CARD | SCR_016602 | CARD, Comprehensive Analysis of RNAi-screen Data | 2026-08-04 09:43:57 | 20 | ||||
|
MetaboAnalystR Resource Report Resource Website 100+ mentions |
MetaboAnalystR (RRID:SCR_016723) | data processing software, data analysis software, software resource, software application, data visualization 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 | 2026-08-04 09:43:58 | 410 | ||||||||
|
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) | data processing software, data analysis software, software resource, software application, data analytics software, software toolkit, data acquisition 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 | 2026-08-04 09:43:57 | 733 | |||||||||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | 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 | 2026-08-04 09:43:58 | 5 | ||||
|
IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:43:57 | 63 | |||||||
|
Sequenza Resource Report Resource Website 50+ mentions |
Sequenza (RRID:SCR_016662) | data processing software, data analysis software, software resource, software application, data visualization 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 | 2026-08-04 09:43:59 | 54 | ||||||||
|
biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | data processing software, data analysis software, software resource, software application, software toolkit | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
NIDDK U54 DE023798; Sloan Foundation 4406J0B; NHGRI R01 HG005220; NSF DBI1053486; NHGRI R01 HG005969; ARO W911NF1110473 |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery, https://bio.tools/biobakery | SCR_016596 | bioBakery, biobakery | 2026-08-04 09:43:57 | 13 | |||||
|
rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data processing software, software application, software resource, data analysis software | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-08-04 09:43:56 | 1 | |||||||||
|
Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | portal, web service, software resource, data access protocol, data or information resource | Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. | global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference |
is affiliated with: PubChem BioAssay is related to: National Library of Medicine has parent organization: NCBI works with: Batch Entrez works with: Biotite |
Free, Freely available | SCR_016640 | 2026-08-04 09:43:57 | 15 | ||||||||||
|
PhenoMeNal Resource Report Resource Website 1+ mentions |
PhenoMeNal (RRID:SCR_016605) | phnmnl, PhenoMeNal | portal, web service, software resource, consortium, data access protocol, organization portal, 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 | 2026-08-04 09:43:57 | 2 | |||||
|
hfoGUI Resource Report Resource Website 1+ mentions |
hfoGUI (RRID:SCR_016726) | hfoGUI | data processing software, data analysis software, signal processing software, software resource, software repository, software application, data visualization software | Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony. | graphical, user, interface, python, processing, data, EEG, LFP, frequency, oscillation | Alzheimer’s Association 2015-NIRG-341570; NIA R01 AG050425 |
Free, Available for download, Freely available | SCR_016726 | hfoGraphical User Interface | 2026-08-04 09:43:58 | 1 | ||||||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | data processing software, data analysis software, software resource, software application, data visualization 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 | 2026-08-04 09:43:56 | 66 | ||||
|
National Sleep Research Resource (NSRR) Resource Report Resource Website 50+ mentions |
National Sleep Research Resource (NSRR) (RRID:SCR_016576) | NSRR | portal, organization portal, data or information resource | 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 | 2026-08-04 09:43:56 | 68 | ||||
|
RColorBrewer Resource Report Resource Website 50+ mentions |
RColorBrewer (RRID:SCR_016697) | data processing software, data visualization software, software application, software resource | Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data. | color, palette, scheme, map, graph, visualize, data |
is used by: ClustVis is affiliated with: CRAN is affiliated with: R Project for Statistical Computing |
Free, Available for download, Freely available | http://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3 | SCR_016697 | 2026-08-04 09:43:58 | 80 | |||||||||
|
Clonotator Resource Report Resource Website |
Clonotator (RRID:SCR_016730) | data processing software, alignment software, data analysis software, web service, software resource, sequence analysis software, software application, data access protocol, image analysis software | Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. | screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data | has parent organization: University of California at San Francisco; California; USA | Free, Freely available, Registration required | https://willseylab.com/clonotator/ | SCR_016730 | 2026-08-04 09:43:58 | 0 | |||||||||
|
Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | image acquisition software, data processing software, portal, storage service resource, software resource, software application, data repository, service resource, data acquisition software, data or information resource | System designed for automated collection of images from a transmission electron microscope. | automated, collection, acquisition, data, image, electron, microscope |
uses: Python Programming Language has parent organization: Scripps Research Institute |
NCRR RR17573; NIGMS GM61939; NSF DBI0352386; NSF DBI9730056; NSF DBI9904547 |
PMID:15890530 | Free, Available for download, Freely available, Registration suggested | SCR_016731 | 2026-08-04 09:43:58 | 42 | ||||||||
|
SCIPION Resource Report Resource Website 10+ mentions |
SCIPION (RRID:SCR_016738) | data processing software, software resource, software application, image processing software, software toolkit | Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe | image, processing, data, 3DEM, macromolecular, complex, electron, microscopy, format, conversion, bio.tools |
is listed by: bio.tools is listed by: Debian |
Spanish Ministry of Economy and Competitiveness ; Comunidad the Madrid ; European Union ; Instruct |
PMID:27108186 | Free, Available for download, Registration required | biotools:monores | https://github.com/I2PC/scipion, https://bio.tools/monores | SCR_016738 | 2026-08-04 09:44:00 | 20 | ||||||
|
NetCirChro Resource Report Resource Website |
NetCirChro (RRID:SCR_016616) | NetCirChro | data processing software, data analysis software, software resource, software application, data visualization 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 | 2026-08-04 09:43:57 | 0 | ||||||||
|
Honolulu-Asia Aging Study of Sleep Apnea Resource Report Resource Website |
Honolulu-Asia Aging Study of Sleep Apnea (RRID:SCR_016587) | HAASSA | topical portal, portal, disease-related portal, data or information resource | 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 | 2026-08-04 09:43:57 | 0 |
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