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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Duke University Omics Data Analysis Core Facility Resource Report Resource Website |
Duke University Omics Data Analysis Core Facility (RRID:SCR_017174) | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource, training service resource | Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies. | bioinformatics, data, analysis, training, expertise, next, generation, sequencing, array, proteomic, omics | has parent organization: Duke University; North Carolina; USA | Restricted | SCR_017174 | Analysis Core, Resource, Core Facility, Genomic Analysis and Bioinformatics, Duke University, Omics Data | 2026-09-12 12:58:49 | 0 | |||||||||
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brainGraph Resource Report Resource Website 10+ mentions |
brainGraph (RRID:SCR_017260) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:50 | 16 | ||||||||
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neuropredict Resource Report Resource Website |
neuropredict (RRID:SCR_017405) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:52 | 0 | ||||||||||
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StatView Version 5.0 Resource Report Resource Website 100+ mentions |
StatView Version 5.0 (RRID:SCR_017411) | data analysis software, data processing software, software application, software resource | Software package for statistical analysis by SAS Institute Inc, Cary, NC. | Statistical, analysis, SAS Institute Inc, , | SCR_017411 | 2026-09-12 12:58:52 | 204 | ||||||||||||
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Mass spectrometry imaging workbench Resource Report Resource Website 100+ mentions |
Mass spectrometry imaging workbench (RRID:SCR_017410) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:52 | 105 | ||||||||
|
ape Resource Report Resource Website 50+ mentions |
ape (RRID:SCR_017343) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:51 | 52 | ||||||
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Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:51 | 16 | |||||||||
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BPC Instruments: Biomethane Potential Test Resource Report Resource Website |
BPC Instruments: 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 | DST ; NRF ; SME ; TIA ; UNESCO ; WRC |
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 | 2026-09-12 12:58:51 | 0 | |||||||
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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, data processing software, software application, software resource | 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 | 2026-09-12 12:58:53 | 0 | |||||||
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redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | analysis service resource, data analysis service, data analysis software, data processing 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 | 2026-09-12 12:58:51 | 5 | ||||||||||
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Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:53 | 0 | ||||||||
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PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:51 | 15 | ||||||||
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Excel Statistics Resource Report Resource Website 10+ mentions |
Excel Statistics (RRID:SCR_017294) | data analytics software, software application, software resource, software toolkit | Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu . | statistical, analysis, BellCurve, Excell | Restricted | SCR_017294 | 2026-09-12 12:58:51 | 29 | |||||||||||
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TWOSEX-MSChart Resource Report Resource Website 10+ mentions |
TWOSEX-MSChart (RRID:SCR_017298) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:51 | 14 | |||||||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | analysis service resource, controlled vocabulary, data analysis service, data or information resource, ontology, production service resource, service 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 | CERCA Program/Generalitat de Catalunya ; European Union ; German Federal Ministry of Education and Research ; NINDS NS36251; Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-09-12 12:58:51 | 187 | |||||||
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Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | 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 | 2026-09-12 12:58:51 | 28 | |||||
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TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | ERC Grant ; EU Seventh Framework Programme |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-09-12 12:58:51 | 166 | ||||||
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Morpheus by Broad Institute Resource Report Resource Website 1000+ mentions |
Morpheus by Broad Institute (RRID:SCR_017386) | data analysis software, data processing software, data visualization 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 | 2026-09-12 12:58:52 | 2141 | |||||||||
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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 | 2026-09-12 12:58:51 | 3 | ||||||||||
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CLC Genomics Server Resource Report Resource Website 10+ mentions |
CLC Genomics Server (RRID:SCR_017396) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:52 | 18 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
