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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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International Human Epigenome Consortium Resource Report Resource Website 10+ mentions |
International Human Epigenome Consortium (RRID:SCR_016937) | IHEC | portal, organization portal, data or information resource, consortium | Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal. | reference, human, epigenome, map, normal, disease, cell, data, quality, standard, sharing |
is related to: 4D Nucleome is related to: Canadian Epigenetics, Environment and Health Research Consortium Network is parent organization of: International Human Epigenome Consortium Data Portal |
Free access to the research community, Open and controlled access to datasets according to policies and guidelines | https://epigenomesportal.ca/ihec/ | SCR_016937 | International Human Epigenome Consortium, IHEC | 2026-08-04 09:44:02 | 26 | |||||||
|
XDSME Resource Report Resource Website 10+ mentions |
XDSME (RRID:SCR_016943) | xdsme | data processing software, software resource, software application, image processing software, software toolkit | Software package of python scripts made to simplify the processing of crystal diffraction images. | simplify, processing, crystal, diffraction, image, data, XDS |
uses: Python Programming Language works with: XDS Program Package |
Free, Available for download, Freely available | SCR_016943 | XDSME, X-ray Detector Software Made Easier, XDS Made Easier | 2026-08-04 09:44:01 | 14 | ||||||||
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Neurolucida 360 Resource Report Resource Website 10+ mentions |
Neurolucida 360 (RRID:SCR_016788) | data processing software, software application, software resource, data analysis software | Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses. | mbf Bioscience, automatic, image, 3D, reconstruction, analysis, neuron, synapse, data | is used by: SPARC Portal | Commercially available, Free trial available | SCR_016788 | 2026-08-04 09:43:59 | 45 | ||||||||||
|
NetworkAnalyst Resource Report Resource Website 500+ mentions |
NetworkAnalyst (RRID:SCR_016909) | data analysis service, data processing software, data analysis software, analysis service resource, web service, software resource, software application, data access protocol, production service resource, service resource, network analysis software | Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data. | gene, expression, profiling, meta, data, analysis, statistical, visual, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25950236 | Free, Freely available, Tutorial available | biotools:networkanalyst | https://bio.tools/networkanalyst | SCR_016909 | 2026-08-04 09:44:00 | 635 | |||||||
|
ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | data processing software, software application, software resource, data analysis software | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIGMS R01 GM067193; NIDA P30 DA018310 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-08-04 09:44:01 | 14 | ||||||
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VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | data processing software, software application, software resource, data analysis software | Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections. | variant, antigen, profiling, data, genome, transcriptome, proteome, gene, expression, infection, Trypanosoma, bio.tools |
is listed by: Debian is listed by: bio.tools requires: Python Programming Language |
Free, Available for download, Freely available | biotools:VAPPER | https://bio.tools/VAPPER | SCR_016993 | VAP, VariantAntigenProfilingPER | 2026-08-04 09:44:02 | 1 | ||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-08-04 09:44:00 | 22 | ||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-08-04 09:44:04 | 53 | ||||||
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CropSight Resource Report Resource Website 1+ mentions |
CropSight (RRID:SCR_016870) | data access protocol, software resource, web service | Software tool which is a PHP and SQL based server platform. Provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management. | PHP, SQL, server, platform, automated, data, collation, storage, information, management, IoT sensor, phenotyping | Free, Available for download, Freely available, Registration required | SCR_016870 | 2026-08-04 09:44:00 | 1 | |||||||||||
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PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | data processing software, data analysis software, software resource, software application, network analysis software | Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. | mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools |
is listed by: Galaxy is listed by: OMICtools is listed by: Debian is listed by: bio.tools works with: Reactome |
European Research Council ; Research Council of Norway ; Bergen Research Foundation ; NIGMS U54 GM114833; NHGRI U41 HG003751 |
DOI:10.1101/375097 | Free, Available for download, Freely available | BioTools:PathwayMatcher, biotools:PathwayMatcher | https://anaconda.org/bioconda/pathwaymatcher, https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher | SCR_016759 | 2026-08-04 09:43:59 | 1 | ||||||
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Growth Profiling Toolbox Resource Report Resource Website |
Growth Profiling Toolbox (RRID:SCR_016878) | data processing software, data analysis software, software resource, software application, software toolkit | Software package as a growth curve automatic processing pipeline in Matlab. | growth, curve, automatic, pipeline, analysis, process, data | Free, Available for download, Freely available | SCR_016878 | 2026-08-04 09:44:00 | 0 | |||||||||||
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Java Treeview Resource Report Resource Website 50+ mentions |
Java Treeview (RRID:SCR_016916) | TreeView | data processing software, data visualization software, software application, software resource | Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure. | gene, expression, data, visualization, microarray, interactive, display, cluster, dataset |
is related to: University of Hamburg; Hamburg; Germany has parent organization: Princeton University; New Jersey; USA |
Free, Available for download, Freely available | https://bitbucket.org/TreeView3Dev/treeview3/ | SCR_016916 | TreeView3, Treeview, Java TreeView | 2026-08-04 09:44:01 | 52 | |||||||
|
sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | data processing software, software application, software resource, data analysis software | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NIDDK R01 DK094699; NHGRI R01 HG006129 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth, https://bio.tools/sleuth, https://bio.tools/sleuth | SCR_016883 | 2026-08-04 09:44:00 | 24 | ||||||
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ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | data processing software, software application, software resource, data analysis software | Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. | multivariate, analysis, feature, selection, omics, data, visualization, regression, classification, variable, exceedes, number, sample, multicollinearity, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | BioTools:ropls, biotools:ropls | https://bio.tools/ropls, https://bio.tools/ropls, https://bio.tools/ropls | SCR_016888 | R Orthogonal Partial Least Squares | 2026-08-04 09:44:01 | 12 | ||||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 1+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | portal, catalog, project portal, database, data or information resource | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIH ; NIDDK |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-08-04 09:44:01 | 9 | ||||||||
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Ragu Resource Report Resource Website 1+ mentions |
Ragu (RRID:SCR_016851) | Ragu | data processing software, software application, software resource, data analysis software | Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics. | statistical, analysis, EEG, MEG, electromagnetic, data, scalp, field | DOI:doi/10.1155/2011/938925 | SCR_016851 | Randomization Graphical User interface, Randomization Graphical User | 2026-08-04 09:44:00 | 3 | |||||||||
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Polyman Resource Report Resource Website 1+ mentions |
Polyman (RRID:SCR_016850) | data processing software, software application, software resource, data analysis software | Software tool as an European Data Format EDF/EDF+ viewer and manual sleep scoring program. Used in EEG and Sleep investigations, but can be used for almost any (also non-medical) sequential time series and event lists. | European, data, format, viewer, manual, sleep, scoring, program, electroencephalography, EEG, EDF, neurophysiology | Free, Available for download, Freely available | SCR_016850 | 2026-08-04 09:44:01 | 2 | |||||||||||
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Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | data processing software, data visualization software, software application, software resource | Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. | quantitative, visualization, aligned, RNA-Seq, read, data, compare, exon, usage, sample, experiment, condition, MISO | is related to: MISO | NCI R01 CA157304; Starr Cancer Consortium ; NIGMS R01 GM096193; NSF IIS 1149662; Alfred P. Sloan research fellowship ; NIGMS R01 GM085319; NCI U01 CA184897; NHGRI R01 HG002439 |
PMID:25617416 DOI:10.1093/bioinformatics/btv034 |
Free, Available for download, Freely available | http://miso.readthedocs.org/en/fastmiso/sashimi.html | SCR_016861 | sashimi_plot | 2026-08-04 09:44:00 | 0 | |||||
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NetworkX Resource Report Resource Website 100+ mentions |
NetworkX (RRID:SCR_016864) | data processing software, data analysis software, software resource, software application, network analysis software | Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | create, analysis, structure, dynamic, function, complex, network, data | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/networkx/networkx | SCR_016864 | 2026-08-04 09:44:00 | 111 | |||||||||
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CellCycleTRACER Resource Report Resource Website Rating or validation data |
CellCycleTRACER (RRID:SCR_017128) | data processing software, data analysis software, web service, software resource, software application, data access protocol | Software tool as supervised machine learning algorithm that classifies and sorts single cell mass cytometry data according to their cell cycle, which allows to correct for cell cycle state and cell volume heterogeneity. Reveals signaling relationships and cell heterogeneity that were otherwise masked. Computational method to quantify cell cycle and cell volume variability. | classify, sort, single, cell, mass, cytometry, data, cycle, state, volume, heterogeneity, quantify, volume, variability | SNSF ; European Research Council ; NIDDK UC4 DK108132; SystemsX MetastasiX grant |
PMID:29434325 | Free, Restricted | SCR_017128 | 2026-08-04 09:44:05 | 0 |
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