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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PremierBiosoft Proteo IQ Software Resource Report Resource Website 10+ mentions |
PremierBiosoft Proteo IQ Software (RRID:SCR_018072) | data processing software, data analysis software, software resource, software application, data analytics software | Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS. | Proteomic, qualitative, quantitative, protein identification, data, PREMIER Biosoft, mass spectrometry data, database search engine |
works with: GenBank works with: UniProtKB works with: IPI |
Restricted | SCR_018072 | ProteoIQ | 2026-08-04 09:44:16 | 34 | |||||||||
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CircaDB Resource Report Resource Website 10+ mentions |
CircaDB (RRID:SCR_018078) | CircaDB | web service, software resource, data access protocol, database, data or information resource | Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans. | Mammalian circadian gene, gene expression, expression profile, mice, human, gene annotation, data, time course expression data | PMID:23180795 | Free, Freely available | http://github.com/itmat/circadb | SCR_018078 | Circadian gene expression profiles DataBase | 2026-08-04 09:44:16 | 19 | |||||||
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QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | data processing software, data analysis software, software resource, software application, software toolkit | Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018076 | Quantify unknown Biophysics | 2026-08-04 09:44:17 | 2 | |||||||||
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Vivli Resource Report Resource Website 1000+ mentions |
Vivli (RRID:SCR_018080) | nonprofit organization, data or information resource, service resource | Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials. | Global data sharing, clinical research data, data, sharing, analytical platform, clinical trial, COVID-19-related trials |
is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is listed by: Data and Computational Resources to Address COVID-19 is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing |
COVID-19 | Doris Duke Charitable Foundation ; Leona M. and Harry B. Helmsley Charitable Trust ; Lyda Hill Philanthropies ; Phrma |
Restricted | DOI:10.17616/R3SB9S, DOI:10.25504/FAIRsharing.uovQrT, DOI:10.25934, r3d100012823 | https://vivli.org/vivli-covid-19-portal-2/, https://doi.org/10.17616/R3SB9S, https://doi.org/10.17616/r3sb9s, https://doi.org/10.25934/, https://dx.doi.org/10.25934/, https://fairsharing.org/10.25504/FAIRsharing.uovQrT, https://doi.org/10.17616/R3SB9S | SCR_018080 | 2026-08-04 09:44:20 | 1532 | ||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | data processing software, data analysis software, software resource, software application, software toolkit | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-08-04 09:44:19 | 6 | |||||||||||
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ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | database, storage service resource, data repository, service resource, catalog, data or information resource | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Union ; SLING 226073; European Commission ; Gen2Phen 200754; NHGRI P41 HG003619 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123, r3d100010222 | http://www.ebi.ac.uk/microarray-as/ae, https://doi.org/10.17616/R3302G | SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2026-08-04 09:40:46 | 7529 | ||||
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Allen Developing Mouse Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Developing Mouse Brain Atlas (RRID:SCR_002990) | expression atlas, reference atlas, atlas, database, data or information resource | Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself. | gene, expression, developing, mouse, brain, pattern, embryonic, postnatal, stage, data, database, reference, atlas, ontology, anatomy, ISH |
is related to: Allen Brain Atlas API is related to: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
PMID:22832508 | Free, Public | nif-0000-00509 | SCR_002990 | Allen Brain Atlas Developing Mouse Brain | 2026-08-04 09:40:47 | 195 | |||||||
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Child Language Data Exchange System (CHILDES) Resource Report Resource Website 10+ mentions |
Child Language Data Exchange System (CHILDES) (RRID:SCR_003241) | CHILDES | storage service resource, software resource, data repository, service resource, database, data or information resource | Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats. | Child, language, conversation, interaction, data, psychology, survey, transcript |
is recommended by: National Library of Medicine has parent organization: Carnegie Mellon University; Pennsylvania; USA works with: TalkBank |
NICHD R01 HD23998; NICHD R01 HD051698 |
PMID:2380278 | Free, Freely available | nif-0000-00624, r3d100010887 | https://doi.org/10.17616/R3M31S | http://childes.psy.cmu.edu | SCR_003241 | Child Language Data Exchange System | 2026-08-04 09:40:51 | 46 | |||
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Digital Access to Scholarship at Harvard Resource Report Resource Website |
Digital Access to Scholarship at Harvard (RRID:SCR_004122) | DASH | storage service resource, data repository, service resource, database, data or information resource | Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH. | scholarship, image, audio clip, video resource, manuscript, data | has parent organization: Harvard University; Cambridge; United States | nlx_158606 | SCR_004122 | 2026-08-04 09:41:03 | 0 | |||||||||
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DbGaP Cleaner Resource Report Resource Website |
DbGaP Cleaner (RRID:SCR_009462) | data processing software, software application, software resource, workflow software | Tool to assist site staff with curation of data dictionary, data item, and subject item files for preparation to uploading and sharing data with DbGaP resource. | gpl-style open source, data, curation, dictionary, sharing, site, tool, workflow software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NCBI database of Genotypes and Phenotypes (dbGap) |
nlx_155609 | SCR_009462 | DbGaP_Cleaner | 2026-08-04 09:42:24 | 0 | |||||||||
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iTools Resource Report Resource Website 10+ mentions |
iTools (RRID:SCR_009626) | iTools | web service, storage service resource, software resource, software repository, data access protocol, data repository, service resource, database, data or information resource | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools, http://www.loni.usc.edu/research/software | http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-08-04 09:42:25 | 45 | |||
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Databrary Resource Report Resource Website 10+ mentions |
Databrary (RRID:SCR_010471) | Databrary | portal, storage service resource, software resource, software repository, data repository, service resource, project portal, database, data or information resource | Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data. | behavior, development, data, sharing, audio track, video |
is listed by: re3data.org is related to: Datavyu is related to: Datavyu has parent organization: New York University; New York; USA has parent organization: Pennsylvania State University |
NSF BCS-1238599; NICHD U01 HD076595 |
Restricted | nlx_157733, r3d100011023 | https://github.com/databrary | SCR_010471 | 2026-08-04 09:42:41 | 13 | ||||||
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Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | data processing software, data analysis software, analysis service resource, software resource, software application, production service resource, service resource, software toolkit | Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data. | Statistic, visualization, data, analysis, quantification, integrated environment, microarray data, RTPCR data, Taqman data, genotype data, copy number data, next generation sequencing data | Free, Available for download, Freely available | OMICS_00850 | https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/ArrayStudio/ArrayStudio/ | http://www.omicsoft.com/array-studio.php | SCR_010970 | 2026-08-04 09:42:48 | 5 | ||||||||
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data processing software, software application, software resource, data analysis software | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-04 09:42:49 | 24583 | ||||||
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pClamp Resource Report Resource Website 5000+ mentions |
pClamp (RRID:SCR_011323) | data processing software, data analysis software, software resource, software application, data acquisition software | Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis. | electrophysiology, data, acquisition, analysis, Molecular Device, voltage, clamp, | is listed by: SoftCite | Commercially available | rid_000085 | https://www.moleculardevices.com/products/axon-patch-clamp-system/acquisition-and-analysis-software/pclamp-software-suite#gref | SCR_011323 | patch clamp, Axon™pCLAMP™ 10 Electrophysiology Data Acquisition and Analysis Software, patch CLAMP, pCLAMP 11, pCLAMP 10, patch Clamp | 2026-08-04 09:42:50 | 9678 | |||||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-08-04 09:42:48 | 5370 | |||||
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sabre Resource Report Resource Website 100+ mentions |
sabre (RRID:SCR_011843) | sabre | data processing software, software application, software resource, data analysis software | Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data. | demultiplex, bardcode, separate, fastq, format, data, next, generation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:sabre, OMICS_01090 | https://bio.tools/sabre | SCR_011843 | Systems Approach to Biomarker Research | 2026-08-04 09:42:52 | 199 | ||||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data processing software, software application, software resource, data analysis software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-04 09:43:05 | 2996 | ||||
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edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data processing software, software application, software resource, data analysis software | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-08-04 09:43:05 | 21899 | ||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | data analysis service, analysis service resource, web service, storage service resource, software resource, data access protocol, production service resource, service resource, data repository, database, data or information resource | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-08-04 09:43:11 | 1239 |
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