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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | production service resource, data analysis service, software application, data processing software, data analysis software, analysis service resource, service resource, software resource | Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data. | microbiome, feature, identify, characterize, analysis, metadata, sample, data | PMID:31239397 | Free, Available for download, Freely available | SCR_017285 | 2026-08-03 09:37:01 | 5 | ||||||||||
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PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | software resource, data processing software, software application, data analysis software | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-08-03 09:36:50 | 15 | ||||||||
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RNAstructure Resource Report Resource Website 10+ mentions |
RNAstructure (RRID:SCR_017216) | production service resource, web service, software application, analysis service resource, simulation software, data access protocol, service resource, software resource | Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. | RNA, DNA, secondary, structure, prediction, analysis |
is listed by: SoftCite has parent organization: University of Rochester; New York; USA |
NIGMS R01 GM076485 | PMID:23620284 | Free, Freely available | SCR_017216 | 2026-08-03 09:37:01 | 42 | ||||||||
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Excel Statistics Resource Report Resource Website 10+ mentions |
Excel Statistics (RRID:SCR_017294) | software toolkit, software resource, software application, data analytics software | Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu . | statistical, analysis, BellCurve, Excell | Restricted | SCR_017294 | 2026-08-03 09:36:35 | 22 | |||||||||||
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PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | software resource, data processing software, software application, data analysis software | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-08-03 09:36:33 | 17 | ||||||
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TWOSEX-MSChart Resource Report Resource Website 10+ mentions |
TWOSEX-MSChart (RRID:SCR_017298) | software resource, data processing software, software application, data analysis software | Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan. | life, table, analysis, development, cohort, population, animal, species, sex | Restricted | SCR_017298 | 2026-08-03 09:36:35 | 12 | |||||||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | ontology, data analysis service, production service resource, service resource, analysis service resource, controlled vocabulary, data or information resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-08-03 09:36:50 | 134 | |||||||
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Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | software toolkit, software application, data processing software, data analysis software, software resource, data visualization software | Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks. | phylogenetic, tree, network, reconstruction, analysis, estimation, Maximum, Likelihood, Parsimony, distance, method, Hadamard conjugation |
is listed by: Debian is listed by: OMICtools is related to: CRAN |
Muséum National D Histoire Naturelle | DOI:10.1093/bioinformatics/btq706 | Free, Available for download, Freely available | OMICS_12497 | https://github.com/KlausVigo/phangorn, https://sources.debian.org/src/r-cran-phangorn/ | SCR_017302 | Phangorn R package | 2026-08-03 09:36:35 | 24 | |||||
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TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | software toolkit, software application, data processing software, data analysis software, software resource | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | EU Seventh Framework Programme ; ERC Grant |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-08-03 09:36:50 | 152 | ||||||
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brainGraph Resource Report Resource Website 10+ mentions |
brainGraph (RRID:SCR_017260) | software resource, data processing software, software application, data analysis software | Software R package for performing graph theory analyses of brain MRI data. | graph, theory, analysis, brain, MRI, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CRAN |
Free, Available for download, Freely available | https://www.nitrc.org/projects/braingraph/, https://rdrr.io/cran/brainGraph/, https://www.r-pkg.org/pkg/brainGraph | SCR_017260 | brainGraph - Graph Theory Analysis of Brain MRI Data in R, brainGraph | 2026-08-03 09:37:01 | 11 | ||||||||
|
neuropredict Resource Report Resource Website |
neuropredict (RRID:SCR_017405) | software resource, data processing software, software application, data analysis software | Software tool for assessment of predictive power, with support for neuroimaging features. Easy machine learning and standardized predictive analysis of biomarkers. | Predictive, analysis, biomarker, neuroimaging, feature | Free, Available for download, Freely available | https://zenodo.org/record/1058993#.XW7ghShKiM8 | SCR_017405 | 2026-08-03 09:36:37 | 0 | ||||||||||
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StatView Version 5.0 Resource Report Resource Website 100+ mentions |
StatView Version 5.0 (RRID:SCR_017411) | software resource, data processing software, software application, data analysis software | Software package for statistical analysis by SAS Institute Inc, Cary, NC. | Statistical, analysis, SAS Institute Inc, , | SCR_017411 | 2026-08-03 09:36:37 | 203 | ||||||||||||
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Mass spectrometry imaging workbench Resource Report Resource Website 50+ mentions |
Mass spectrometry imaging workbench (RRID:SCR_017410) | software resource, data processing software, software application, data analysis software | Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging. | Analysis, mass, spectrometry, imaging, data, Galaxy, framework, imzML, file, quality, control, visualization, statistics, docker, container | is related to: University of Freiburg; Baden-Wurttemberg; Germany | DOI:10.1101/628719 | Free, Available for download, Freely available | https://github.com/foellmelanie/docker-galaxy-msi, https://galaxyproject.org/use/msi/ | SCR_017410 | 2026-08-03 09:36:51 | 98 | ||||||||
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DIANA-mirExTra Resource Report Resource Website 1+ mentions |
DIANA-mirExTra (RRID:SCR_017498) | production service resource, web service, analysis service resource, data access protocol, service resource, software resource | Software tool for analysis of expression data for microRNA function. | Analysis, expression, data, microRNA, function, DIANA tool | is provided by: DIANA Tools | Free, Freely available | http://diana.imis.athena-innovation.gr/DianaTools/ | SCR_017498 | Mirextra 2.0 | 2026-08-03 09:36:39 | 1 | ||||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | portal, production service resource, service resource, analysis service resource, data or information resource, software resource | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; NIDCD R01 DC013817; NIMH R24 MH114815; Hearing Health Foundation (Hearing Restoration Project) |
Restricted | SCR_017467 | gene Expression Analysis Resource | 2026-08-03 09:37:03 | 76 | |||||||
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cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | production service resource, software application, data processing software, analysis service resource, image analysis software, service resource, software resource | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | Cell, population, microscopy, image, network, analysis, quantify, structure, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Free, Freely available | SCR_017465 | 2026-08-03 09:36:51 | 0 | |||||||||
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Analysis, Visualization, and Informatics Lab-space (AnVIL) Resource Report Resource Website 10+ mentions |
Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) | AnVIL | data repository, portal, data or information resource, storage service resource, service resource, project portal | Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces. | Dataset, NHGRI, program, NIH, initiative, funded, human, genomic, data, access, sharing, FAIR, analysis, workflow |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIH | Restricted | https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL | SCR_017469 | Visualization, and Informatics Lab-space, AnVIL, Analysis Visualization and Informatics Lab-space, Analysis | 2026-08-03 09:36:38 | 24 | ||||||
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Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | software resource, data processing software, software application, data analysis software | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-08-03 09:36:51 | 0 | |||||||
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shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | production service resource, web application, analysis service resource, service resource, software resource | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo | SCR_017605 | 2026-08-03 09:36:41 | 0 | ||||||
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Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | software resource, data processing software, software application, data analysis software | Analysis and modeling code for waves of seizure activity. | Analysis, modeling, wave, seizure, brain, activity, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1451384 | Free, Freely available | SCR_017455 | SeizureWaves, Seizure Waves, Seizure-Waves | 2026-08-03 09:36:38 | 0 |
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