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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data analysis software, data processing software, software application, software resource | 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 |
Harris and IBS Honours scholarships ; Independent Research Institutes Infrastructure Support Scheme 361646; Melbourne International Research Scholarship ; NHMRC 406657; Victorian State Government OIS grant |
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 | 2026-09-12 12:57:53 | 23868 | ||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:57:53 | 3073 | ||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service | 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 | 2026-09-12 12:58:02 | 1324 | ||||||
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Databrary Resource Report Resource Website 10+ mentions |
Databrary (RRID:SCR_010471) | Databrary | data or information resource, data repository, database, portal, project portal, service resource, software repository, software resource, storage service 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 |
NICHD U01 HD076595; NSF BCS-1238599 |
Restricted | nlx_157733, r3d100011023 | https://github.com/databrary | SCR_010471 | 2026-09-12 12:57:19 | 17 | ||||||
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Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software 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 | 2026-09-12 12:57:27 | 5 | ||||||||
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:57:26 | 27197 | ||||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 |
Foundation Leducq Transatlantic Network Grant ; NCI CA52599; NIDDK DK063491; NIGMS P50 GM081892; NIH HC088093; NURSA consortium grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-09-12 12:57:25 | 5929 | |||||
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dbEST Resource Report Resource Website 100+ mentions |
dbEST (RRID:SCR_008132) | data or information resource, data repository, database, service resource, storage service resource | Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms. | data, sequence, single, pass, cDNA, express, tag, bio.tools, gold standard |
is listed by: Debian is listed by: bio.tools has parent organization: NCBI |
PMID:8401577 | biotools:dbest, nif-0000-20937, r3d100010648 | http://www.ncbi.nlm.nih.gov/dbEST/, https://bio.tools/dbest, https://doi.org/10.17616/R3FG8P | SCR_008132 | database Expressed Sequence Tag (EST), database Expressed Sequence Tag | 2026-09-12 12:57:00 | 186 | |||||||
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GeneNetWorks Resource Report Resource Website 1+ mentions |
GeneNetWorks (RRID:SCR_008034) | data acquisition software, data analysis software, data or information resource, data processing software, data visualization software, database, software application, software resource | GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses. | experimental, expression, gene, gene regulation, genetic, analysis, data, dna, graphical, molecular, navigation, network, program, protein, rna, software, system | nif-0000-10232 | SCR_008034 | GNW | 2026-09-12 12:56:59 | 1 | ||||||||||
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Genomatix Software: Understanding Gene Regulation Resource Report Resource Website 500+ mentions |
Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) | data analysis software, data or information resource, data processing software, database, narrative resource, portal, short course material, software application, software resource, topical portal, training material | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 13,2026. Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc. | effect, expression, functional, gene, genome, alignment, analysis, annotation, biological, cascade, cell, data, dna, in-silico analysis, mechanism, metabolic pathway, microarray, mining, molecular, network, pathway, promoter, protein, region, regulation, scientific, sequence, signaling, software, stimulus, systems biology, technology, text mining, transcription, FASEB list | has parent organization: Genomatix Solutions | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10236 | http://www.genomatix.de/products/index.html | SCR_008036 | Genomatix | 2026-09-12 12:56:59 | 887 | |||||||
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Distributed Annotation System Resource Report Resource Website 10+ mentions |
Distributed Annotation System (RRID:SCR_008427) | data or information resource, narrative resource, software resource, standard specification | The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center. | annotation, database, software, genomic, protein, sequence, visualization, data, client-server, integration, bioinformatics, genome, structure, data integration |
is listed by: 3DVC has parent organization: Uppsala University; Uppsala; Sweden |
Howard Hughes Medical Institute ; NHGRI 2-P01-HG00956 |
nif-0000-30177 | SCR_008427 | BioDAS | 2026-09-12 12:57:04 | 11 | ||||||||
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DE-ID Data Corp Resource Report Resource Website 1+ mentions |
DE-ID Data Corp (RRID:SCR_008668) | software resource | A commercial organization that suppplies software which creates separate HIPAA-compliant repositories of de-identified patient records and reports. This software allows clinicians, researchers, and administrative leadership to safely access, search, share, and analyze de-identified patient-level data. DE-ID can be acquired as stand-alone tool or integrated with data networks or clinical information systems. | clinical, data, patient protection, surgical report | nif-0000-33387 | SCR_008668 | DE-ID Data Corp | 2026-09-12 12:57:07 | 1 | ||||||||||
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GeneTraffic Resource Report Resource Website 10+ mentions |
GeneTraffic (RRID:SCR_008651) | data analysis software, data management software, data processing software, software application, software resource | GeneTraffic is a web-based microarray data analysis and management software developed by Iobion Informatics that allows users to log onto a server, upload their microarray data and perform analysis and project management remotely. GeneTraffic was made by Iobion Informatics (now under Stratagene) and can be accessed thorough Internet Explorer 6.0 or greater on Windows XP. | gene, data, management, microarray, software | nif-0000-33028 | SCR_008651 | 2026-09-12 12:57:07 | 24 | |||||||||||
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OpenTox Framework Resource Report Resource Website |
OpenTox Framework (RRID:SCR_008686) | OT | data or information resource | Tools for the integration of data from various sources (public and confidential), for the generation and validation of computer models for toxic effects, libraries for the development and seamless integration of new algorithms, and scientifically sound validation routines. The goal of OpenTox is to develop an interoperable predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications. OpenTox is relevent for users from a variety of research areas: Toxicological and chemical experts (e.g. risk assessors, drug designers, researchers) computer model developers and algorithm developers non specialists requiring access to Predictive Toxicology models and data OpenTox applications can combine multiple web services providing users access to distributed toxicological resources including data, computer models, validation and reporting. Applications are based on use cases that satisfy user needs in predictive toxicology. OpenTox was initiated as a collaborative project involving a combination of different enterprise, university and government research groups to design and build the initial OpenTox framework. Additionally numerous organizations with industry, regulatory or expert interests are active in providing guidance and direction. The goal is to expand OpenTox as a community project enabling additional expert and user participants to be involved in developments in as timely a manner as possible. To this end, our mission is to carry out developments in an open and transparent manner from the early days of the project, and to open up discussions and development to the global community at large, who may either participate in developments or provide user perspectives. Cooperation on data standards, data integration, ontologies, integration of algorithm predictions from different methods, and testing and validation all have significant collaboration opportunities and benefits for the community. OpenTox is working to meet the requirements of the REACH legislation using alternative testing methods to contribute to the reduction of animal experiments for toxicity testing. Relevant international authorities (e.g., ECB, ECVAM, US EPA, US FDA) and industry organizations participate actively in the advisory board of the OpenTox project and provide input for the continuing development of requirement definitions and standards for data, knowledge and model exchange. OpenTox actively supports the development and validation of in silico models and algorithms by improving the interoperability between individual systems (common standards for data and model exchange), increasing the reproducibility of in silico models (by providing a quality source of structures, toxicity data and algorithms) and by providing scientifically sound and easy-to-use validation routines. OpenTox is committed to the support and integration of alternative testing methods using in vitro assay approaches, systems biology, stem cell technology, and the mining and analysis of human epidemiological data. Hence the framework design must take into account extensibility to satisfy a broad range of scientific developments and use cases. | drug, epidemiolgical, experiment, framework, alogrithm, animal, application, assay, chemical, computer, data, human, interoperable, in vitro, knowledge, method, mining, model, platform, researcher, stem cell, systems biology, technology, testing, toxicicty, toxicology, validation, ontology | European Union FP7 | nif-0000-33775 | SCR_008686 | 2026-09-12 12:57:07 | 0 | |||||||||
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Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource Resource Report Resource Website |
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource (RRID:SCR_015324) | access service resource, analysis service resource, core facility, data or information resource, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data. | hematology, bioinformatics, explore, understand, genomic, data, cancer |
is listed by: NIDDK Information Network (dkNET) has parent organization: Fred Hutchinson Cancer Center |
Cancer | NIDDK P30 DK056465 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015907 | SCR_015324 | Hutch, Bioinformatic Resource, Fred, Co-operative Center for Excellence in Hematology, Cancer Center | 2026-09-12 12:58:26 | 0 | ||||||
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Cerebrovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) | CDKP | data or information resource, database, disease-related portal, portal, topical portal | Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data. | human, genetic, information, cerebrovascular, disease, data, knowledge |
is listed by: NIDDK Information Network (dkNET) has parent organization: Massachusetts General Hospital Labs and Facilities |
cerebrovascular disease | Accelerating Medicines Partnership in Type 2 Diabetes ; NIH ; NINDS |
Free, Available for download | SCR_016535 | SCR_015628 | Cerebrovascular Disease Knowledge Portal (CDKP) | 2026-09-12 12:58:28 | 17 | |||||
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BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | data processing software, data visualization software, software application, software resource, web application | Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. | Box plot generation, customized box plot, data, plot, analysis |
is listed by: SoftCite is related to: PlotsOfData is related to: vioplot |
ERC ; Genome Québec International Recruitment Award ; Wellcome Trust ; WTCCB |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | 2026-09-12 12:58:28 | 370 | ||||||
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BOINC - Berkeley Open Infrastructure for Network Computing Resource Report Resource Website 1+ mentions |
BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) | BOINC | data acquisition software, data distribution software, data or information resource, data processing software, portal, project portal, software application, software resource | Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science. | infrastructure, computing, network, volunteer, data, application, distribution, storage, communication, biology, medicine, physics, astronomy, computer science | has parent organization: University of California at Berkeley; Berkeley; USA | PMID:27547555 | Open source, Free, Available for download, The public can contribute to this resource, The research community can contribute to this resource, Available on Google Play Store, Available on Kindle Store, Available on Amazon App Store | SCR_015896 | Berkeley Open Infrastructure for Network Computing, Berkeley Open Infrastructure for Network Computing (BOINC) | 2026-09-12 12:58:32 | 3 | |||||||
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redcap-importer Resource Report Resource Website |
redcap-importer (RRID:SCR_016032) | data acquisition software, data processing software, software application, software resource | Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import. | automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, import | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016032 | 2026-09-12 12:58:34 | 0 | |||||||||
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Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1; Wellcome Trust WT098051 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | 2026-09-12 12:58:33 | 56 |
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