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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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gdpc Resource Report Resource Website |
gdpc (RRID:SCR_016119) | data processing software, data visualization software, software application, software resource | Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame. | visualizing, output, data, molecular, dynamic, simulation, animation, visualization |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_19946 | https://sources.debian.org/src/gdpc/ | http://www.frantz.fi/software/gdpc.php, https://directory.fsf.org/wiki/Gdpc | SCR_016119 | 2026-08-04 09:43:48 | 0 | |||||||
|
Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | data processing software, software application, software resource, data analysis software | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | GNU Datamash | 2026-08-04 09:43:47 | 2 | |||||||
|
PhonBank Resource Report Resource Website 1+ mentions |
PhonBank (RRID:SCR_016312) | storage service resource, data repository, service resource | Database for study of early phonological development using Phon program. Child phonology component of TalkBank system. | Data, early, phonological, development, Phon, program, child |
is recommended by: National Library of Medicine is related to: TalkBank |
NICHD R01 HD051698 | Free, Freely available | SCR_016312 | 2026-08-04 09:43:51 | 2 | |||||||||
|
National Children's Study (NCS) Archive Resource Report Resource Website |
National Children's Study (NCS) Archive (RRID:SCR_016311) | NCS Archive | storage service resource, data repository, service resource | Data and sample repository for National Children's Study. Provides access to data and samples collected from over 5,600 U.S. birth families to study environmental influences on child health and development. Data and biological and environmental samples are freely available, with approved request, for scientific research. | data, repository, children, child, family, study, research, health, pediatric, growth, development | is recommended by: National Library of Medicine | NICHD | Restricted | https://ncsarchive.s-3.net/ | SCR_016311 | National Children's Study, National Children's Study Archive | 2026-08-04 09:43:53 | 0 | ||||||
|
cOMet Resource Report Resource Website 1+ mentions |
cOMet (RRID:SCR_016276) | software application, software resource, data management software | Software for error correction of optical mapping data. | optical, mapping, error, correction, data, visual, image | Free, Available for download | SCR_016276 | 2026-08-04 09:43:51 | 3 | |||||||||||
|
NeuroXM Brain Science Suite Resource Report Resource Website |
NeuroXM Brain Science Suite (RRID:SCR_016372) | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data. | semantic, data, graph, neuroscience, neuroanatomy, ontology, circuitry, pathway, multimodal, brain | Commercially available | SCR_016372 | Brain Science Suite, NeuroXM, NeuroXM Suite | 2026-08-04 09:43:54 | 0 | ||||||||||
|
Research Data Management Platform Resource Report Resource Website 1+ mentions |
Research Data Management Platform (RRID:SCR_016268) | RDMP | data management software, storage service resource, software resource, software application, data repository, service resource, software toolkit, data or information resource | Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”. | metadata, reproducibility, anonymization, security, audit, clinical, dataset, translational, research, data, management, catalogue, health, informatics, linkage | has parent organization: University of Dundee; Scotland; United Kingdom | Medical Research Council (MRC) MR/M501633/1; Wellcome Trust WT086113; EU Horizon 2020 633983 |
Free, Available for download | https://hic.dundee.ac.uk/Installers/RDMP/Stable/ | SCR_016268 | 2026-08-04 09:43:52 | 2 | |||||||
|
Starbase V2.0 Resource Report Resource Website 500+ mentions |
Starbase V2.0 (RRID:SCR_016303) | web application, software resource | Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes. | visualize, analyze, discover, download, large, genomic, data, set, miRNA, RNA-RNA, protein-RNA, interaction, network, decoding, CLIP-Seq, Degradome-Seq | Ministry of Science and Technology of China ; National Basic Research Program No. 2011CB811300 |
PMID:24297251 | Free, Freely available, Available for download | SCR_016303 | 2026-08-04 09:43:51 | 819 | |||||||||
|
Fractalis Resource Report Resource Website 1+ mentions |
Fractalis (RRID:SCR_016362) | data analysis service, data processing software, analysis service resource, web service, software resource, data access protocol, software application, software library, production service resource, service resource, data visualization software, software toolkit | Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis. | platform, independent, interactive, visual, analysis, biomedical, data, library | National Centre of Excellence in Research on Parkinson’s disease NCER13/BM/11264123; Luxembourg Ministry of Higher Education and Research |
Free, Available for download, Freely available | https://git-r3lab.uni.lu/Fractalis/fractalis/blob/master/README.md | SCR_016362 | 2026-08-04 09:43:52 | 1 | |||||||||
|
lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | data processing software, data analysis software, software resource, software application, software toolkit | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373; NICHD R01 HD084633 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-08-04 09:43:53 | 3 | |||||||
|
bioSyntax Resource Report Resource Website 1+ mentions |
bioSyntax (RRID:SCR_016207) | software application, software resource, data management software | Software for syntax highlighting for computational biology. | computation, syntax, language, code, scientific, data, workflow, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1186/s12859-018-2315-y | Free, Available for download | biotools:biosyntax, OMICS_25594 | https://github.com/bioSyntax/bioSyntax, https://bio.tools/biosyntax, https://sources.debian.org/src/biosyntax/ | SCR_016207 | 2026-08-04 09:43:50 | 2 | |||||||
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The Pancreatic Beta-Cell Consortium Resource Report Resource Website 1+ mentions |
The Pancreatic Beta-Cell Consortium (RRID:SCR_016328) | PBC Consortium | portal, topical portal, storage service resource, disease-related portal, data repository, service resource, data or information resource | Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells. | repository, pancreatic, Bcell, data, whole, cell, model, human, connect, contribute, model, idea, diabetes, integrate, approach, computation, design, effective, treatment, experiment, biology |
is related to: University of Southern California; Los Angeles; USA is related to: California Institute of Technology; Division of Biology is related to: University of California at Berkeley; Berkeley; USA is related to: Scripps Research Institute |
Diabetes | SCR_016328 | Pancreatic B Cell Consortium | 2026-08-04 09:43:52 | 4 | ||||||||
|
The Bergen fMRI Toolbox Plugin for EEGLab Resource Report Resource Website 1+ mentions |
The Bergen fMRI Toolbox Plugin for EEGLab (RRID:SCR_016335) | data processing software, data analysis software, software resource, software application, software toolkit | Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts. | correct, gradient, artifact, data, electrophysiology, functional, magnetic, resonance, imaging, neuroscience |
is related to: EEGLAB is related to: MATLAB has parent organization: University of Bergen; Bergen; Norway |
Free, Available for download, Freely available | SCR_016335 | 2026-08-04 09:43:52 | 1 | ||||||||||
|
Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data processing software, data analysis software, software resource, software application, software toolkit | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | NIH DP2 HD088158; Alfred P. Sloan Foundation Research Fellowship |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-08-04 09:43:52 | 203 | ||||||||
|
Electrographic Seizure Analyzer Resource Report Resource Website 1+ mentions |
Electrographic Seizure Analyzer (RRID:SCR_016344) | data processing software, software application, software resource, data analysis software | Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting. | automate, analysis, electrographic, seizure, EEG, LFP, data, event, detection, parameter, setting | is related to: MATLAB | Free, Available for download, Freely available | SCR_016344 | 2026-08-04 09:43:52 | 5 | ||||||||||
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jVenn Resource Report Resource Website 100+ mentions |
jVenn (RRID:SCR_016343) | data processing software, data analysis software, software resource, software application, data visualization software | JavaScript plug-in software application for web environments to analyze data. It is an interactive Venn diagram viewer.Used for comparing lists with Venn Diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. | analyze, data, Venn, diagram, visualisation, independent, platform | is related to: VennDiagram | Free, Available for download, Freely available | http://bioinfo.genotoul.fr/jvenn | SCR_016343 | 2026-08-04 09:43:53 | 248 | |||||||||
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Rtsne Resource Report Resource Website 100+ mentions |
Rtsne (RRID:SCR_016342) | data processing software, software resource, software application, data visualization software, software toolkit | Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation. | data, visualisation, high-dimentional, van der Maaten, Barnes-Hut, implementation, distribution, stochastic, neighbor, embedding |
is listed by: CRAN is related to: R Project for Statistical Computing is related to: University of Toronto; Ontario; Canada |
the Netherlands Organization for Scientific Research (NWO) ; European Union Seventh Framework Program |
Free, Available for download, Freely available | SCR_016900 | https://cran.r-project.org/web/packages/Rtsne/index.html | SCR_016342 | , R t-distributed stochastic neighbor embedding, R t-Distributed Stochastic Neighbor Embedding | 2026-08-04 09:43:52 | 176 | ||||||
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BioJupies Resource Report Resource Website 50+ mentions |
BioJupies (RRID:SCR_016346) | web application, software resource | Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text. | automatically, generate, RNAseq, data, analysis, notebook, create, visualize, report, custom, raw, processed, user, interface | is affiliated with: Icahn School of Medicine at Mount Sinai; New York; USA | Free, Available for download, Freely available | SCR_016346 | 2026-08-04 09:43:53 | 65 | ||||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | data processing software, data analysis software, software resource, software application, software toolkit | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | NIH DP2 DE023321; NIBIB R01 EB008400; Bill and Melinda Gates Foundation OPP1032317 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-08-04 09:43:53 | 86 | ||||||
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MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | portal, storage service resource, data repository, service resource, data or information resource | Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020. | analysis, exploration, metagenomic, metatranscriptomic, amplicon, assembly, data, sequence, ENA, microbial, population, environment, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) |
the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the European Commission within the Research Infrastructures programme of Horizon 2020 676559; InnovateUK 102513; Research Councils UK (RCUK) ; EMBL ; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; EU Seventh Framework Programme for Research MICROB3 |
PMID:31696235 | Free, Freely available, Training online available | r3d100011192, biotools:MGnify | https://bio.tools/MGnify, https://doi.org/10.17616/R34W68 | SCR_016429 | , MGnify, EBI Metagenomics | 2026-08-04 09:43:53 | 51 |
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