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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mass spectrometry imaging workbench Resource Report Resource Website 50+ mentions |
Mass spectrometry imaging workbench (RRID:SCR_017410) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:25 | 98 | ||||||||
|
ape Resource Report Resource Website 10+ mentions |
ape (RRID:SCR_017343) | data analysis software, software resource, data processing software, software application | Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R. | analysis, phylogenetics, evolution, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: CRAN |
PMID:30016406 PMID:14734327 PMID:22495750 |
Free, Available for download, Freely available | biotools:ape | https://cran.r-project.org/web/packages/ape/ape.pdf http://ape-package.ird.fr/ https://bio.tools/ape |
SCR_017343 | ape 3.0, ape 5.0, Analysis of Phylogenetics and Evolution | 2026-02-14 02:03:24 | 42 | ||||||
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Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | data analysis software, software resource, data processing software, software application | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-02-14 02:03:11 | 15 | |||||||||
|
Biomethane Potential Test Resource Report Resource Website |
Biomethane Potential Test (RRID:SCR_017319) | BMP, BMP Test, AMPTS | instrument resource | Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry. | Anaerobic digestion, waste to energy, waste management, renewable energies, biogas, biomethane, modelling, University of Johannesburg (UJ), UJ-PEETS, Quantification, characterization, analysis, AI-2 import system permease protein lsrC | has parent organization: University of Johannesburg; Johannesburg; South Africa | TIA ; DST ; WRC ; NRF ; UNESCO ; SME |
https://www.uj.ac.za/faculties/febe/peets | SCR_017319 | , Automatic Methane Potential Test System (AMPTS) II, Biomethane Potential Test System, Automatic Methane Potential Test System | 2026-02-14 02:03:11 | 0 | |||||||
|
redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | data processing software, data analysis service, analysis service resource, data analysis software, production service resource, service resource, software application, 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 | 2026-02-14 02:03:10 | 5 | ||||||||||
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PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:18 | 15 | ||||||||
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Excel Statistics Resource Report Resource Website 10+ mentions |
Excel Statistics (RRID:SCR_017294) | data analytics software, software resource, software toolkit, software application | Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu . | statistical, analysis, BellCurve, Excell | Restricted | SCR_017294 | 2026-02-14 02:03:18 | 22 | |||||||||||
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TWOSEX-MSChart Resource Report Resource Website 10+ mentions |
TWOSEX-MSChart (RRID:SCR_017298) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:23 | 12 | |||||||||||
|
SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | ontology, data analysis service, analysis service resource, data or information resource, production service resource, service resource, controlled vocabulary | 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 | 2026-02-14 02:03:26 | 134 | |||||||
|
Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | data visualization software, data processing software, data analysis software, software toolkit, software application, software resource | 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 | 2026-02-14 02:03:11 | 24 | |||||
|
TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data processing software, data analysis software, software toolkit, software application, 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 | 2026-02-14 02:03:23 | 152 | ||||||
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Morpheus by Broad Institute Resource Report Resource Website 1000+ mentions |
Morpheus by Broad Institute (RRID:SCR_017386) | data visualization software, data processing software, data analysis software, service resource, software application, software resource | Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis. | Matrix, visualization, analysis, heatmap, input, data, Java | has parent organization: Broad Institute | Free, Available for download, Freely available | https://github.com/cmap/morpheus.js | SCR_017386 | 2026-02-14 02:03:24 | 1704 | |||||||||
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Brainreader Resource Report Resource Website 1+ mentions |
Brainreader (RRID:SCR_017308) | software resource | Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain. | Company, Denmark, medical, image, analysis, processing, software, brain | is affiliated with: Neuroreader | SCR_017308 | brainreader, BrainReader | 2026-02-14 02:03:26 | 3 | ||||||||||
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CLC Genomics Server Resource Report Resource Website 10+ mentions |
CLC Genomics Server (RRID:SCR_017396) | data analysis software, software resource, data processing software, software application | Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler. | high, throughput, sequencing, analysis, data | works with: CLC Genomics Workbench | Restricted | SCR_017396 | 2026-02-14 02:03:12 | 18 | ||||||||||
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DIANA-mirExTra Resource Report Resource Website 1+ mentions |
DIANA-mirExTra (RRID:SCR_017498) | web service, analysis service resource, production service resource, service resource, data access protocol, 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 | 2026-02-14 02:03:28 | 1 | ||||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | portal, analysis service resource, data or information resource, production service resource, service 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 | 2026-02-14 02:03:20 | 76 | |||||||
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cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | data processing software, analysis service resource, production service resource, service resource, software application, software resource, image analysis software | 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 | 2026-02-14 02:03:25 | 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, storage service resource, portal, data or information 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 | 2026-02-14 02:03:12 | 24 | ||||||
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LAN toolbox Resource Report Resource Website 1+ mentions |
LAN toolbox (RRID:SCR_017629) | LANtoolbox | data processing software, data analysis software, software toolkit, time-series analysis software, software application, software resource, 1d time-series analysis software | Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB. | Neuroscientist, data, EEG, experimental, analysis, code, script | is related to: MATLAB | Free, Available for download, Freely available | SCR_017629 | Laboratory of Analysis in Neurosciences Toolbox, EEG Toolbox | 2026-02-14 02:03:14 | 2 | ||||||||
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Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:25 | 0 |
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