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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, software resource, data processing software, software application | 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 | 2026-02-13 10:57:01 | 21899 | ||||
|
PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | data repository, storage service resource, web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | 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 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-02-13 10:57:06 | 1239 | ||||||
|
Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | community building portal, portal, software development tool, software development environment, data or information resource, software application, software resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-02-13 10:57:04 | 24 | ||||
|
Computational Biology at ORNL Resource Report Resource Website |
Computational Biology at ORNL (RRID:SCR_005710) | Computational Biology at ORNL | data analysis service, production service resource, service resource, analysis service resource | We are the Computational Biology and Bioinformatics Group of the Biosciences Division of Oak Ridge National Laboratory. We conduct genetics research and system development in genomic sequencing, computational genome analysis, and computational protein structure analysis. We provide bioinformatics and analytic services and resources to collaborators, predict prospective gene and protein models for analysis, provide user services for the general community, including computer-annotated genomes in Genome Channel. Our collaborators include the Joint Genome Institute, ORNL''s Computer Science and Mathematics Division, the Tennessee Mouse Genome Consortium, the Joint Institute for Biological Sciences, and ORNL''s Genome Science and Technology Graduate Program. | genetics, research, system development, genomic sequencing, computation, genome analysis, protein structure, analysis, gene, protein, gene annotation, annotation, genome | has parent organization: Oak Ridge National Laboratory | nlx_149161 | SCR_005710 | Computational Biology at Oak Ridge National Laboratory, Computational Biology and Bioinformatics Group at ORNL, Computational Biology Bioinformatics Group at ORNL | 2026-02-13 10:55:40 | 0 | ||||||||
|
Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | data analysis service, production service resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-02-13 10:55:42 | 6 | ||||
|
The Guardian: Science Resource Report Resource Website |
The Guardian: Science (RRID:SCR_005166) | Guardian: Science | data or information resource, narrative resource, blog | Latest science news, comment, analysis and features from guardian.co.uk, the world''s leading liberal voice. | science, news, comment, analysis, space, medicine, genetics, medical research |
is used by: NIF Data Federation is used by: Integrated Blogs |
nlx_144198 | SCR_005166 | 2026-02-13 10:55:35 | 0 | |||||||||
|
Scientific American Observations Resource Report Resource Website |
Scientific American Observations (RRID:SCR_005195) | SA Observations | data or information resource, narrative resource, blog | From the editors and reporters of Scientific American, this blog delivers commentary, opinion and analysis on the latest developments in science and technology and their influence on society and policy. From reasoned arguments and cultural critiques to personal and skeptical takes on interesting science news, you''ll find a wide range of scientifically relevant insights here. | commentary, opinion, analysis, science, technology, society, policy |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: Scientific American |
nlx_144201 | SCR_005195 | Scientific American - Observations | 2026-02-13 10:55:35 | 0 | ||||||||
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FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products Resource Report Resource Website |
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products (RRID:SCR_005738) | FuSSiMeG | data analysis service, production service resource, service resource, analysis service resource | FuSSiMeG is being discontinued, may not be working properly. Please use our new tool ProteinOn. Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins. Platform: Online tool | protein, similarity, gene ontology, gene, ontology, statistical analysis, term enrichment, semantic similarity, analysis, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: ProteInOn has parent organization: University of Lisbon; Lisbon; Portugal |
Free for academic use | nlx_149198 | SCR_005738 | Functional Semantic Similarity Measure between Gene-Products, Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) | 2026-02-13 10:55:41 | 0 | |||||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 100+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | data analysis service, production service resource, service resource, analysis service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-02-13 10:55:56 | 492 | |||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | data analysis service, production service resource, service resource, analysis service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-02-13 10:55:48 | 3 | |||||
|
SPIKE Resource Report Resource Website 100+ mentions |
SPIKE (RRID:SCR_010466) | SPIKE | data or information resource, service resource, database | Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways | visualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, ear, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: ConsensusPathDB has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Cancer | A-T Children's Project ; Wolfson Foundation ; European Union FP7 ; Israel Science Foundation |
PMID:21097778 PMID:18289391 |
biotools:spike, nlx_157705 | https://bio.tools/spike | SCR_010466 | Signaling Pathway Integrated Knowledge Engine | 2026-02-13 10:56:42 | 128 | ||||
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Phenotypes and Mutant Alleles Resource Report Resource Website 10+ mentions |
Phenotypes and Mutant Alleles (RRID:SCR_017523) | data or information resource, service resource, database | Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes. | MGI, phenotype, human, disease, analysis, model, genetically, engineered, mutation, strain, specific, phenotype, data | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017523 | Phenotypes, Alleles & Disease Models | 2026-02-13 10:58:04 | 11 | |||||||||
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University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility Resource Report Resource Website |
University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) | MidSouth Bioinformatics Center, MBC | core facility, software resource, access service resource, service resource | Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice. | bioinformatics, assistance, consulting, training, analysis, omic, data | has parent organization: University of Arkansas; Arkansas; USA | Open | SCR_017168 | Bioinformatics Center, , University of Arkansas, UA, Core Facility, MBC, UALR, MidSouth, Little Rock | 2026-02-13 10:57:52 | 0 | ||||||||
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ROIs selection with a non-graphical user interface Resource Report Resource Website 1+ mentions |
ROIs selection with a non-graphical user interface (RRID:SCR_016352) | data access protocol, software resource, application programming interface | It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets. | non graphical, user, interface, keyboard, callback, function, analysis, big, data, set | is related to: MATLAB | Free, Available for download, Freely available | https://ptrrupprecht.wordpress.com/2015/06/24/a-simple-non-graphical-user-interface-in-matlab-keyboard-callback-functions/ | SCR_016352 | 2026-02-13 10:57:48 | 2 | |||||||||
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PlantGSEA Resource Report Resource Website 10+ mentions |
PlantGSEA (RRID:SCR_016866) | PlantGSEA | data analysis service, production service resource, service resource, analysis service resource | Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. | gene, set, enrichement, analysis, plant | Ministry of Science and Technology of China ; Ministry of Education of China |
DOI:10.1093/nar/gkt281 | SCR_016866 | The Plant GeneSet Enrichment Analysis Toolkit, Plant GeneSet Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-02-13 10:57:47 | 17 | ||||||||
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software resource, software toolkit | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-02-13 10:54:39 | 31 | ||||||||
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Acquisition and Analysis for Electron Tomography Resource Report Resource Website |
Acquisition and Analysis for Electron Tomography (RRID:SCR_000192) | TOM Toolbox | software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1) | electron microscope, electron tomography, acquisition, alignment, analysis, processing, reconstruction, software, alignment, reconstruction, processing | has parent organization: Max Planck Institute of Biochemistry; Martinsried; Germany | PMID:15721576 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10145 | http://www.biochem.mpg.de/en/rd/baumeister/tom_e/ | SCR_000192 | TOM software toolbox | 2026-02-13 10:54:38 | 0 | |||||
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TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software resource, software application | MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7 | disease target, drug discovery, drug, matlab, gene network, genetic interaction, gene, drug screening, mutation driver, therapeutic target, drug candidate, compound, mapping, analysis | has parent organization: Biomedical Simulations Resource | Cancer | NIBIB P41-EB001978 | PMID:22952662 | Free, Under the terms of a Release Agreement., Please cite | nlx_152573 | http://bmsr.usc.edu/Software/TARGET/TARGET.html | SCR_001392 | 2026-02-13 10:54:50 | 7 | ||||
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DPARSF Resource Report Resource Website 500+ mentions |
DPARSF (RRID:SCR_002372) | DPARSF | data processing software, software resource, software toolkit, software application | A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely. | magnetic resonance, fmri, resting-state fmri, matlab, analysis, brain |
is used by: DPABI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: RFMRI.ORG |
PMID:20577591 | GNU General Public License | nlx_155735 | http://www.nitrc.org/projects/dparsf | SCR_002372 | Data Processing Assistant for Resting-State fMRI | 2026-02-13 10:55:01 | 564 | |||||
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Fusion ICA Toolbox Resource Report Resource Website 10+ mentions |
Fusion ICA Toolbox (RRID:SCR_003494) | FIT | data processing software, software resource, software toolkit, software application | A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 | analysis, functional magnetic resonance imaging, cca, image, eeg, neuroimaging, matlab, smri, snp, mri, algorithm, reusable library, independent component analysis, principal component analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of New Mexico; New Mexico; USA |
NIBIB 1RO1EB005846; NSF 0612076 |
GNU General Public License | nif-0000-36743 | http://www.nitrc.org/projects/fit | SCR_003494 | Fusion ICA Toolbox (FIT) | 2026-02-13 10:55:15 | 13 |
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