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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-09-12 12:59:08 | 56 | ||||||||
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Leica QWin Resource Report Resource Website 1+ mentions |
Leica QWin (RRID:SCR_018940) | data processing software, image analysis software, image processing software, software application, software resource | Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional. | Leica, microscope, digital camera, image analysis, image processing, quantitative microscopy | is listed by: SoftCite | Restricted | http://www.mcbainsystems.com/pdf/Leica_QWin.pdf | SCR_018940 | 2026-09-12 12:59:08 | 5 | |||||||||
|
PAST Resource Report Resource Website 100+ mentions |
PAST (RRID:SCR_019129) | data analysis software, data processing software, software application, software resource | Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy. | Paleontological statistics, data analysis, data manipulation function, data plotting, multivariate statistics, ecological analysis, spatial analysis, morphometrics, stratography | is listed by: SoftCite | Free, Available for download, Freely available | SCR_019129 | PAST 4.03, PAleontological STatistics | 2026-09-12 12:59:10 | 153 | |||||||||
|
MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. | Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide |
uses: Mascot is listed by: SoftCite |
Free, Available for download | http://msquant.alwaysdata.net/ | SCR_019206 | 2026-09-12 12:59:10 | 4 | |||||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, data processing software, software application, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-09-12 12:59:10 | 2879 | ||||||
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Epi Info Resource Report Resource Website 10+ mentions |
Epi Info (RRID:SCR_021682) | data analysis software, data analytics software, data processing software, software application, software resource, software toolkit | Software suite of interoperable software tools designed for global community of public health practitioners and researchers. Provides easy data entry form and database construction, customized data entry experience, and data analysis with epidemiologic statistics, maps, and graphs for public health professionals who may lack information technology background.Statistical software for epidemiology developed by Centers for Disease Control and Prevention in Atlanta, Georgia. Available for Microsoft Windows, Android and iOS, along with web and cloud version. | Centers for Disease Control and Prevention, data analysis, epidemiologic statistics, maps, graphs, public health professionals tools | is listed by: SoftCite | Free, Available for download, Freely available | SCR_021682 | Epi Info TM, Epi Info™, Epi Info 6, Epi Info 7 | 2026-09-12 01:00:00 | 35 | |||||||||
|
Heidelberg Eye Explorer Resource Report Resource Website 10+ mentions |
Heidelberg Eye Explorer (RRID:SCR_022045) | data management software, software application, software resource | Platform that centralizes management of ophthalmic images. HEYEX interfaces with electronic medical record systems and third-party devices to allow exchange, storage, and dynamic review of diagnostic images. Heidelberg Engineering imaging products use Heidelberg Eye Explorer software platform and database to store patient information and images. | ophthalmic images management, Heidelberg Engineering imaging products, software to store patient information, software to store images | is listed by: SoftCite | Free, Available for download, Freely available | https://www.eyeoptics.dk//files/pdf/heidelberg/hrt_3_brochure_-_three_pearls_in_one_shell_english.pdf, https://business-lounge.heidelbergengineering.com/us/en/products/heidelberg-eye-explorer/heyex-2/downloads/#downloads | SCR_022045 | HEYEX 2, HEYEX | 2026-09-12 01:00:04 | 16 | ||||||||
|
MATLAB Resource Report Resource Website 10000+ mentions |
MATLAB (RRID:SCR_001622) | MATLAB | data processing software, image processing software, programming language, software application, software resource | Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance. | computing, analyze, visualization, algorithm, plot, vector, matrix |
uses: Functional Network Connectivity (FNC) uses: MVGC Multivariate Granger Causality Matlab Toolbox uses: UltraMegaSort 2000 uses: Elastica2D uses: OSort uses: COMPASS is used by: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) is used by: Orientation Distribution Function in Constant Solid Angle (CSA-ODF) is used by: NiiStat is used by: NeuroElf is used by: MRIcroS is used by: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity is used by: GIMME is used by: GazeReader is used by: Efficient Permutation Testing is used by: APERTURE is used by: Tscratch is used by: PreSurgMapp is used by: SimTracker is used by: ICASSO is used by: TherMos is used by: Mixed Effect Model of Genetic-Set and Environment Interaction is used by: FMAToolbox is used by: BABAM is used by: Soma-Segmentation is used by: SpiSOP is used by: CHIPS is used by: GrowthToolbox is used by: RNAcompete is used by: MicrobeTracker is used by: Sound Analysis Pro is used by: Vocal Inventory Clustering Engine (VoICE) is used by: Automatic Analysis is used by: Measurement Control And Data Analysis Software is used by: Fluorescent Imaging Analysis Software FIMAS is used by: GEMB is used by: IronClust is used by: PAM is used by: calciumImagingAnalysis is used by: TractionsForAll is used by: DeePVP is used by: FieldTrip is used by: Protofilament Bending Models is used by: Toolkit for MIRA LAB Striatal Segmentation is used by: EvaluateMuscleTissueWithElastography is used by: Microscopy_tif_Channel_Quant_MATLAB is used by: CARNet TFA Function is listed by: SoftCite is related to: Spatio- Spectro- Temporal Receptive Field is related to: Extensible MATLAB Medical image Analysis is related to: MultiPhase-SEG is related to: An Open-Source MATLAB-to-Python Compiler is related to: Mastrave modelling library is related to: Libeep EEGLAB plugin is related to: The Bergen fMRI Toolbox Plugin for EEGLab is related to: Electrographic Seizure Analyzer is related to: BVA import/export EEGLAB plugin is related to: ROIs selection with a non-graphical user interface is related to: Reglo ICC control with Matlab is related to: QModeling is related to: MicroFilament Analyzer is related to: Letswave is related to: KiloSort is related to: Suite2P is related to: kCSD-Matlab is related to: nonparametricGGC_toolbox is related to: User Friendly Functional Connectivity - UF²C is related to: Frozen Noise is related to: Microscopy Image Browser is related to: MrDiffusion is related to: rsfMRI_fconn calculation is related to: SPM is related to: Colour maps for brain imaging is related to: Tools for NIfTI and ANALYZE image is related to: PESTO is related to: PPR-Meta is related to: NMF Toolbox is related to: SynapseLocator is related to: SBFSEM-tools is related to: Brain Gene Expression Analysis toolbox is related to: Neural Ideal is related to: Computer Vision System Toolbox is related to: LAN toolbox is related to: hMRI-toolbox is related to: Brainstorm is related to: auto_acpc_reorient is related to: SuperSegger is related to: MNE software is related to: Toolbox for Representational Similarity Analysis is related to: Sandwich Estimator Toolbox is related to: alpha helix coordinate frame simulation is related to: ZebEyeTrack is related to: PottersWheel is related to: Calliope calcium imaging processing package is related to: MVPA Light is related to: Amsterdam Decoding And Modeling is related to: Residue Iteration Decomposition is related to: ObjectFinder is related to: Deep Learning Toolbox is required by: OSort is required by: COMPASS is required by: MicrobeTracker is required by: Wave_clus is required by: Mass Univariate ERP Toolbox is required by: Linear Fascicle Evaluation is required by: PALM works with: CoSMoMVPA works with: Nexus works with: Empirical Gramian Framework works with: OriginPro works with: circular statistics works with: MRspa works with: shiTools |
PMID:30609523 PMID:21934110 |
Restricted | nlx_153890 | SCR_001622 | matlab, MATLAB -The Language of Technical Computing, MATLAB, matrix laboratory | 2026-09-12 01:00:07 | 66533 | ||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NIGMS RC2 GM092519; NIH ; NIMH ; NINDS ; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; Wellcome Trust Strategic Award 095931 |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, SCR_018407, nif-0000-30467 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-09-12 01:00:09 | 29025 | ||||
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Statgraphics Centurion Resource Report Resource Website 1+ mentions |
Statgraphics Centurion (RRID:SCR_015248) | data analysis software, data processing software, data visualization software, software application, software resource | Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers. | statistical analysis software, statistical visualization software, statistical analysis | is listed by: SoftCite | Available for download, Trial available, Available for purchase | SCR_015248 | Statgraphics Centurion XVII | 2026-09-12 12:58:26 | 7 | |||||||||
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MPlus Resource Report Resource Website 1000+ mentions |
MPlus (RRID:SCR_015578) | data analysis software, data processing software, simulation software, software application, software resource | Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data. | statistical modeling software, data imaging software, software model, modeling estimator, modeling algorithms | is listed by: SoftCite | Available for purchase, Free demo available, Student pricing is available | SCR_015578 | Mplus Version 8 | 2026-09-12 12:58:28 | 1032 | |||||||||
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MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canada Research Chairs Program ; Canadian Institutes for Health Research ; Genome Alberta ; Genome Canada ; McGill University ; Natural Sciences and Engineering Research Council of Canada |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-09-12 12:58:27 | 13689 | |||||
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X!Tandem Resource Report Resource Website 10+ mentions |
X!Tandem (RRID:SCR_015645) | data analysis software, data processing software, software application, software resource | Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences. | Search engine, command line tool, matching tandem mass spectra, peptide sequence, protein sequence, protein identification, tandem mass spectrum, xml file, FASEB list |
is listed by: SoftCite is related to: XTandem Parser |
Free, Available for download, Freely available | SCR_018388 | SCR_015645 | 2026-09-12 12:58:28 | 47 | |||||||||
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JASP Resource Report Resource Website 1000+ mentions |
JASP (RRID:SCR_015823) | data analysis software, data processing software, software application, software resource | Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests. | statistical analysis, data analysis, statistical test, frequentist analysis, bayesian analysis, r package |
uses: R Project for Statistical Computing is listed by: SoftCite |
European Research Council | PMID:28685272 | Open source, Free, Available for download, Tutorial available, Runs on Windows, Runs on MAC OS, Runs on Linux | https://github.com/jasp-stats/jasp-desktop | SCR_015823 | 2026-09-12 12:58:31 | 4695 | |||||||
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MCODE Resource Report Resource Website 1000+ mentions |
MCODE (RRID:SCR_015828) | algorithm resource, data analysis software, data processing software, image analysis software, software application, software resource | Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks. | cluster, clustering, graph analysis, network, network topology, interconnectivity | is listed by: SoftCite | Canadian Institutes of Health Research (CIHR) ; MDS-Sciex ; Ontario Research and Development Challenge Fund |
PMID:12525261 PMID:25570063 |
Free, Available for download | http://baderlab.org/Software/MCODE | SCR_015828 | 2026-09-12 12:58:31 | 1254 | |||||||
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Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-09-12 12:58:32 | 83 | ||||||
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Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-09-12 12:58:33 | 1261 | ||||||
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BRASS Resource Report Resource Website 10+ mentions |
BRASS (RRID:SCR_017091) | data analysis software, data processing software, software application, software resource | Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements. | analysis, BAM, file, paired, end, sequencing, determine, rearrangement, breakpoint, assemble |
is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | SCR_017091 | 2026-09-12 12:58:48 | 47 | ||||||||||
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Google Resource Report Resource Website 100+ mentions |
Google (RRID:SCR_017097) | commercial organization | American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook. | technology, company, internet, service, product, search, engine, cloud, computing, software, hardware, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is parent organization of: golang |
grid.420451.6, Crossref funder ID: 100006785, ISNI, Wikidata: Q95, biotools:Google | https://ror.org/00njsd438, https://bio.tools/Google | SCR_017097 | Google LLC | 2026-09-12 12:58:48 | 437 | ||||||||
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OMTools Resource Report Resource Website 1+ mentions |
OMTools (RRID:SCR_017143) | alignment software, data analysis software, data processing software, data visualization software, image analysis software, software application, software resource, software toolkit | Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles. | optical, mapping, data, processing, analysis, visualization, large, scale, profile, phylogenesis | is listed by: SoftCite | Chinese University of Hong Kong ; Food and Health Bureau of the Hong Kong Special Administrative Region ; HKSAR Research Grants Council ; Lee Hysan Foundation ; Lo Kwee-Seong Biomedical Research Fund |
PMID:28505226 | Free, Available for download, Freely available | SCR_017143 | 2026-09-12 12:58:49 | 2 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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