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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility Resource Report Resource Website |
Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility (RRID:SCR_017160) | core facility, access service resource, data analysis service, analysis service resource, software resource, production service resource, service resource | Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing. | bioinformatics, biocomputing, sequencing, data, omics, analysis, visualization, management | has parent organization: Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany | Restricted | SCR_017160 | , Bioinformatics Facility, Core Facility, Bioinformatics Core Facility, Epigenetics, Max Planck Institiute of Immunobiology | 2026-02-16 09:49:10 | 0 | |||||||||
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CytExpert Software Resource Report Resource Website 500+ mentions |
CytExpert Software (RRID:SCR_017217) | software application, data processing software, data analysis software, software resource, data acquisition software | Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter. | control, instrument, data, collection, analysis, CytoFLEX Platform, Beckman Coulter, flow, cytometry |
is listed by: OMICtools works with: Beckman Coulter CytoFLEX LX Flow Cytometer |
OMICS_30185 | SCR_017217 | 2026-02-16 09:49:11 | 888 | ||||||||||
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PennAI Resource Report Resource Website |
PennAI (RRID:SCR_017215) | software application, data processing software, data visualization software, data analysis software, data management software, software resource | Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems. | Supervised, machine, learning, technique, data, mining, storing, analysis, visualizationn, artificial, intelligence | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | http://pennai.org/ https://epistasislab.github.io/pennai/ |
SCR_017215 | Accessible artificial intelligence from University of Pennsylvania | 2026-02-16 09:49:11 | 0 | ||||||||
|
University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility Resource Report Resource Website |
University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility (RRID:SCR_017173) | CGAT | training service resource, core facility, access service resource, data analysis service, analysis service resource, production service resource, service resource, data or information resource | Core provides genomics training, as well as assistance in next generation sequencing analyses. | bioinformatics, genomics, next, generation, sequencing, data, analysis | has parent organization: University of Oxford; Oxford; United Kingdom | Restricted | SCR_017173 | Medical Sciences Division, Computational Genomics: Analysis and Training Core Facility, CGAT, University of Oxford, Computational Genomics Analysis and Training Core Facility | 2026-02-16 09:49:10 | 0 | ||||||||
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Montreal Clinical Research Bioinformatics Core Facility Resource Report Resource Website |
Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) | IRCM BIF, BIF | training service resource, core facility, access service resource, data analysis service, analysis service resource, production service resource, service resource, data or information resource | Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses. | bioinformatics, genomic, omics, data, analysis, RNA-Seq, CHIP-Seq, RIP-Seq, DNA, methylation, DNA-Seq, rRNA, microarray | Restricted | SCR_017176 | , Institute of Clinical Research of Montreal, IRCM, Bioinformatics Core Facility, BIF | 2026-02-16 09:49:11 | 0 | |||||||||
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Centre for Genome Regulation Bioinformatics Core Facility Resource Report Resource Website |
Centre for Genome Regulation Bioinformatics Core Facility (RRID:SCR_017145) | Biocore CRG | training resource, core facility, access service resource, software resource, service resource | Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations. | bioinformatics, NGS, consultation, data, analysis, next, generation, sequencing | has parent organization: Centre for Genomic Regulation; Barcelona; Spain | Restricted | SCR_017145 | Bioinformatics Core, , Core Facility, Centre for Genomic Regulation, Biocore, CRG | 2026-02-16 09:49:10 | 0 | ||||||||
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Bruker WinEPR program Resource Report Resource Website 1+ mentions |
Bruker WinEPR program (RRID:SCR_017023) | software application, data processing software, data analysis software, software resource, data acquisition software | Software tool to operate the EMX series of spectrometers by Bruker. Provides rapid data analysis of 1D and 2D data sets, provides environment for acquisition and processing of CW-EPR and CW-ENDOR spectra with the EMXplus and EMXmicro series of spectrometers. | operate, EMX, serie, spectrophotometer, Bruker, data, analysis, 1D, 2D, dataset, acquisition, processing, CW-EPR, CW-ENDOR | Commercially available | SCR_017023 | 2026-02-16 09:49:08 | 1 | |||||||||||
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OMTools Resource Report Resource Website 1+ mentions |
OMTools (RRID:SCR_017143) | software application, data processing software, software toolkit, data visualization software, data analysis software, image analysis software, software resource, alignment software | Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles. | optical, mapping, data, processing, analysis, visualization, large, scale, profile, phylogenesis | is listed by: SoftCite | Food and Health Bureau of the Hong Kong Special Administrative Region ; Chinese University of Hong Kong ; HKSAR Research Grants Council ; Lo Kwee-Seong Biomedical Research Fund ; Lee Hysan Foundation |
PMID:28505226 | Free, Available for download, Freely available | SCR_017143 | 2026-02-16 09:49:10 | 2 | ||||||||
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PCAGO Resource Report Resource Website 1+ mentions |
PCAGO (RRID:SCR_017033) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options. | analysis, RNAseq, read, count, data, principal, component, analysis, PCA, agglomerative, clustering, normalization, filtering, gene, annotation, visualization | is listed by: OMICtools | Deutsche Forschungsgemeinschaft (DFG) ; International Leibniz Research School for Microbial and Biomolecular Interactions |
DOI:10.1101/433078 | Free, Freely available | OMICS_32232 | SCR_017033 | 2026-02-16 09:49:09 | 7 | |||||||
|
NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_017248) | NAT | software application, data processing software, data visualization software, data analysis software, software resource, 3d visualization software | Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons. | 3D, visualization, analysis, data, image, single, neuron, tracing |
is listed by: OMICtools is related to: R Project for Statistical Computing has parent organization: MRC Laboratory of Molecular Biology |
Restricted | OMICS_18884 | http://jefferislab.github.io. https://CRAN.R-project.org/package=nat |
SCR_017248 | nat, , NeuroAnatomy Toolbox | 2026-02-16 09:49:11 | 4 | ||||||
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pKiss Resource Report Resource Website 1+ mentions |
pKiss (RRID:SCR_017256) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool for folding RNA secondary structures, including two limited classes of pseudoknots. Performs abstract shape analysis for structures holding pseudoknots up to complexity of kissing hairpin motifs. Successor of pknotsRG. Used for secondary structure prediction including kissing hairpin motifs. | folding, RNA, secondary, structure, pseudoknot, abstract, shape, analysis, hairpin, motif | is listed by: OMICtools | PMID:25273103 | Free, Available for download, Freely available | SCR_017256 | pKISS | 2026-02-16 09:49:12 | 4 | ||||||||
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Deep Blue Epigenomic Data Server Resource Report Resource Website 1+ mentions |
Deep Blue Epigenomic Data Server (RRID:SCR_017490) | web service, access service resource, data access protocol, software resource, service resource, data or information resource | Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis. | Data, epigenomic, collection, ontology, storing, distributing, organizing, retriving, searching, genetic, metadata, analysis |
uses: ENCODE uses: Blueprint Epigenome uses: NIH Roadmap is related to: Roadmap Epigenomics Project |
German Science Ministry ; EU |
Free, Freely available | SCR_017490 | 2026-02-16 09:49:15 | 2 | |||||||||
|
DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
European Social Fund ; John S. Latsis Public Benefit Foundation ; Development Grants For Research Institutions – KRIPIS ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; European Regional Development Fund |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/ http://www.microrna.gr/miRPathv3 https://bio.tools/diana-mirpath |
http://www.microrna.gr/miRPathv2 | SCR_017354 | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-02-16 09:49:13 | 366 | ||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-02-16 09:49:13 | 7 | ||||||||
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microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | software application, data processing software, image processing software, image analysis software, software resource | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | Image, guided, mass, spectrometry, automatic, cell, finding, point, based, registration, whole, slide, image, analysis, processing, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIDA DA018310; NIMH U01 MH109062; National Science Foundation Graduate Research Fellowship Program ; Springborn Fellowship ; NIGMS T32 GM070421 |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-02-16 09:49:14 | 1 | |||||||
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Relacs Resource Report Resource Website 1+ mentions |
Relacs (RRID:SCR_017280) | software application, data processing software, data analysis software, software resource, data acquisition software | Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings. | data, acquisition, analysis, electrophysiology, neuronal, response, control, stimulation | Free, Available for download, Freely available | SCR_017280 | Control, and Stimulation, Relaxed Electrophysiological Data Acquisition | 2026-02-16 09:49:12 | 2 | ||||||||||
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Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | software application, data processing software, data visualization software, data analysis software, image analysis software, software resource, 3d visualization software, segmentation software | Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience. | MBF Bioscience, vasculature, reconstruction, image, analysis, 3D, vessel, data, automatic, quantify, anastomoses, microvascular |
is used by: SPARC Portal works with: Vesselucida Explorer |
Restrcited | https://learn.mbfbioscience.com/vle.html | SCR_017320 | Vesselucida 360, Vesselucida | 2026-02-16 09:49:12 | 2 | |||||||
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | software application, data processing software, data visualization software, data analysis software, software resource | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Viertel Fellowship ; Victorian State Government Operational Infrastructure Support and Australian Government |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-02-16 09:49:13 | 23 | ||||||||
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BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
Royal Society of New Zealand Marsden award ; European Research Council ; NIGMS U01 GM110749; Swiss National Science foundation ; Max Planck Society ; EMBL |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-02-16 09:49:12 | 194 | |||||||
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SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-02-16 09:49:12 | 2 |
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