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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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wavethresh Resource Report Resource Website 1+ mentions |
wavethresh (RRID:SCR_024311) | software resource, software toolkit | Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation. | perform 1D, 2D and 3D real and complex valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage, data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-wavethresh/ | SCR_024311 | 2026-09-03 05:00:50 | 3 | |||||||||
|
PMAP Resource Report Resource Website |
PMAP (RRID:SCR_000740) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers. | proteolytic pathway, proteolysis, database, data | has parent organization: Sanford Burnham Prebys Medical Discovery Institute | PMID:18842634 PMID:16448029 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03318 | SCR_000740 | 2026-09-03 05:01:00 | 0 | ||||||||
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Cancer Gene Index Resource Report Resource Website 1+ mentions |
Cancer Gene Index (RRID:SCR_001117) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data. | gene, cancer, genetics, pharmacology, disease, database, data |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01575 | SCR_001117 | 2026-09-03 05:01:38 | 2 | ||||||||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-09-03 04:52:19 | 1 | |||||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, service resource, storage service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-09-03 04:47:03 | 15598 | ||||||
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FigShare Resource Report Resource Website 1000+ mentions |
FigShare (RRID:SCR_004328) | figshare | data or information resource, data repository, database, service resource, storage service resource | Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy. | collection, repository, figure, theses, publication, poster, presentation, fileset, dataset, video, negative, data, FASEB list |
is used by: PrePubMed is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: STRENDA is listed by: FORCE11 is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing is related to: ImpactStory is related to: Overleaf is related to: FigsharePlus is related to: NIH Figshare Archive is parent organization of: TRAMS |
Digital Science | Free with charges for advance features, Available for download, Freely available | DOI:10.17616/R3PK5R, DOI:10.6084, r3d100010066, nlx_34569, DOI:10.25504/FAIRsharing.drtwnh | http://www.force11.org/node/4794, https://doi.org/10.17616/R3PK5R, https://doi.org/10.17616/r3HP4V, https://doi.org/10.6084/, https://dx.doi.org/10.6084/, https://fairsharing.org/10.25504/FAIRsharing.drtwnh, https://doi.org/10.17616/R3PK5R | SCR_004328 | Fig share, Figshare | 2026-09-03 04:47:09 | 1467 | |||||
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Eukaryotic Pathogen Database Resources Resource Report Resource Website 10+ mentions |
Eukaryotic Pathogen Database Resources (RRID:SCR_004512) | EuPathDB, ApiDB | data access protocol, data or information resource, data repository, database, portal, service resource, software resource, storage service resource, topical portal, web service | EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens. | Data, Apicomplexa, parasitic, protozoa, Cryptosporidium, Plasmodium, Toxoplasma, database, pathogen, dataset, FASEB list |
is listed by: NIH Data Sharing Repositories is related to: ApiDots is related to: NIH Data Sharing Repositories is related to: AmoebaDB is related to: MicrobiomeDB has parent organization: University of Georgia; Georgia; USA is parent organization of: FungiDB is parent organization of: TriTrypDB is parent organization of: PlasmoDB is parent organization of: ApiDB ToxoDB is parent organization of: ApiDB CryptoDB |
malaria, kala-azar, african sleeping sickness, chagas disease, aids-related, aids | Bill and Melinda Gates Foundation ; Wellcome Trust ; NIAID |
PMID:19914931 PMID:17098930 |
nlx_49652, r3d100011557 | http://ApiDB.org, https://doi.org/10.17616/R3X06F | SCR_004512 | EuPath, Apicomplexan Database Resources, Eukaryotic Pathogen Genome Database, EuPathDB, Eukaryotic Pathogen Database Resources, ApiDB, Apicomplexan Database | 2026-09-03 04:47:19 | 39 | ||||
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European Molecular Biology Laboratory Resource Report Resource Website 5000+ mentions |
European Molecular Biology Laboratory (RRID:SCR_004473) | EMBL | data or information resource, graduate program resource, organization portal, portal, postdoctoral program resource, training resource | Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states. | molecular, biology, medicine, data, training, service, organization, data, technology, academic |
is related to: GenBank is related to: EU-AIMS is related to: EMIF is related to: 3D-Beacons is parent organization of: EMBL - Bork Group is parent organization of: PTMcode is parent organization of: eggNOG is parent organization of: Eukaryotic Linear Motif is parent organization of: BreakDB is parent organization of: SIDER is parent organization of: DELLY is parent organization of: European Bioinformatics Institute is parent organization of: STRING is parent organization of: PEMer is parent organization of: HTSeq is parent organization of: OGEE - Online GEne Essentiality database is parent organization of: Expression Database in 4D is parent organization of: DSMM - a Database of Simulated Molecular Motions is parent organization of: FUNPEP is parent organization of: Search Tool for Interactions of Chemicals is parent organization of: AltSplice Database of Alternative Spliced Events is parent organization of: Candidate Genes to Inherited Diseases is parent organization of: Washington University Basic Local Alignment Search Tool is parent organization of: Secondary Structure Matching is parent organization of: Agadir is parent organization of: Bork Group's WU-BLAST2 Search Service at EMBL is parent organization of: FoldX is parent organization of: BioModels.net is parent organization of: CopySeq is parent organization of: miRNA is parent organization of: htseq-count is parent organization of: MOCAT is parent organization of: Human-gpDB is parent organization of: easyRNASeq is parent organization of: Transeq is parent organization of: PhenoMeNal |
nlx_46173 | SCR_004473 | European Molecular Biology Laboratory, EMBL | 2026-09-03 04:47:08 | 5410 | ||||||||
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FieldTrip Resource Report Resource Website 1000+ mentions |
FieldTrip (RRID:SCR_004849) | data analysis software, data processing software, software application, software resource, software toolkit | Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists. | MEG, EEG, iEEG, analysis, data, time, frequency, source, reconstruction, dipole, beamformers, non parametric, statistical, testing |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Connectome Coordination Facility has parent organization: Radboud University; Nijmegen; The Netherlands works with: CoSMoMVPA works with: SleepTrip works with: EEGLAB works with: SPM |
Human Connectome project ; Netherlands Ministry of Economic Affairs ; Netherlands Ministry of Education Culture and Science ; NIH Blueprint for Neuroscience Research |
PMID:21253357 | Free, Available for download, Freely available, Tutorial available | nlx_143928 | http://www.nitrc.org/projects/fieldtrip | SCR_004849 | 2026-09-03 04:47:43 | 3297 | ||||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-09-03 04:47:44 | 17718 | ||||
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riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data analysis software, data processing software, software application, software resource | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-09-03 04:54:09 | 4 | ||||||||||
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Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | alignment software, data analysis software, data processing software, image analysis software, software application, software resource | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian Government ; Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-09-03 04:54:02 | 203 | ||||||
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scran Resource Report Resource Website 100+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, data processing software, software application, software resource | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; EMBL ; National Health and Medical Research Council of Australia |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-09-03 04:53:58 | 100 | ||||
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OptiQuant Software Resource Report Resource Website 1+ mentions |
OptiQuant Software (RRID:SCR_016769) | data acquisition software, data analysis software, data processing software, image acquisition software, image analysis software, software application, software resource | Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer. | image, acquisition, analysis, display, archiving, quantify, autoradiography, data, PerkinElmer | Commercially available, Free download available | https://optiquant.software.informer.com/5.0/ | SCR_016769 | OptiQuant, OptiQuant 3.0, OptiQuant software 5.0, OptiQuant 5.0 | 2026-09-03 04:54:13 | 4 | |||||||||
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mixOmics Resource Report Resource Website 50+ mentions |
mixOmics (RRID:SCR_016889) | data analysis software, data processing software, software application, software resource | Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multivariate, exploration, integration, biological, dataset, variable, selection, analysis, data, high, throughput, sequencing, technology, spectral, imaging |
is related to: R Project for Statistical Computing has parent organization: University of Melbourne; Victoria; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016889 | 2026-09-03 04:54:09 | 61 | ||||||||||
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BISE Resource Report Resource Website 10+ mentions |
BISE (RRID:SCR_016774) | analysis service resource, data or information resource, database, organization portal, portal, production service resource, service resource, software resource | Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows. | bioimage, analysis, data, information, image, processing, algorithm, workflow, bio.tools |
lists: FibrilTool is listed by: Debian is listed by: bio.tools has parent organization: NEUBIAS |
Free, Freely available, Registration required | biotools:BISE | https://bio.tools/BISE | SCR_016774 | 2026-09-03 04:53:56 | 13 | ||||||||
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Tools for NIfTI and ANALYZE image Resource Report Resource Website 1+ mentions |
Tools for NIfTI and ANALYZE image (RRID:SCR_016895) | data analysis software, data processing software, image analysis software, service resource, software application, software resource, software toolkit | Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform. | neuroimaging, data, program, analysis, image |
is related to: NIfTI Data Format Working Group is related to: MATLAB |
Free, Available for download, Freely available | https://perso.telecom-paristech.fr/bloch/P6Image/Projets/Nez2/NIfTI_matlab_tools/NIfTI_tools.pdf | SCR_016895 | Neuroimaging Informatics Technology Initiative (NIfTI) and Analyze Image data | 2026-09-03 04:54:16 | 1 | ||||||||
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FlowSOM Resource Report Resource Website 100+ mentions |
FlowSOM (RRID:SCR_016899) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. | flow, cytometry, data, analysis, self, organizing, map, marker, cell, detect, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing is a plug in for: FlowJo |
PMID:25573116 | Free, Available for download, Freely available | biotools:flowsom | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html, https://www.flowjo.com/exchange/#/plugin/profile?id=7, https://bio.tools/flowsom | SCR_016899 | FlowSOM, Flow Self Organizing Map | 2026-09-03 04:54:08 | 125 | ||||||
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FRETBursts Resource Report Resource Website 1+ mentions |
FRETBursts (RRID:SCR_016898) | FRETBursts | data analysis software, data processing software, software application, software resource, software toolkit | Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data. | freely, diffusing, single, molecule, FRET, smFRET, cellular, process, intermolecular, interaction, conformational, change, biomacromolecule, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM069709; NIGMS R01 GM95904 |
PMID:27532626 | Free, Available for download, Freely available | biotools:fretbursts | https://opensmfs.github.io/FRETBursts/, https://bio.tools/fretbursts | SCR_016898 | Förster Resonance Energy Transfer Bursts, FRETBursts | 2026-09-03 04:53:56 | 3 | ||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | data analysis software, data processing software, image analysis software, software application, software resource | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-09-03 04:54:09 | 18 |
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