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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MOLEonline Resource Report Resource Website 10+ mentions |
MOLEonline (RRID:SCR_018314) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features. | biomacromolecular channel, analysis, biomacromolecular pore, biomacromolecular tunnel, transmembrane pore analysis, analysis, biomacromolecular sturcture, physicochemical feature |
works with: PDBe - Protein Data Bank in Europe works with: CSA - Catalytic Site Atlas works with: UniProt |
PMID:29718451 | Free, Freely available | https://mole.upol.cz/online/ | http://old.mole.upol.cz/ | SCR_018314 | MOLEonline 2.0 | 2026-09-12 12:58:59 | 36 | ||||||
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Proteomic Data Commons Resource Report Resource Website 100+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | analysis service resource, data or information resource, data repository, database, production service resource, service resource, storage service resource | Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication. | Cancer, proteomic, data, precision medicine, diagnosis, treatment, analysis, biospeciment, clinical data, metadata |
is related to: Cancer Research Data Commons has parent organization: National Cancer Institute |
cancer | Restricted | SCR_018273 | 2026-09-12 12:58:59 | 102 | ||||||||
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Interactive Repeated Experiments Dotplot Resource Report Resource Website |
Interactive Repeated Experiments Dotplot (RRID:SCR_018328) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments. | Interactive graphic, repeated independent experiment, repeated experiment data, graph, analysis, dot plot | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018328 | 2026-09-12 12:59:00 | 0 | |||||||||
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Watchdog Resource Report Resource Website 1+ mentions |
Watchdog (RRID:SCR_018355) | data analysis software, data management software, data processing software, software application, software resource | Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent. | Workflow management system, automated data analysis, next generation sequencing, large scale experimental data, analysis | Free, Available for download, Freely available | https://github.com/klugem/watchdog, https://anaconda.org/bioconda/watchdog-wms | SCR_018355 | 2026-09-12 12:59:00 | 2 | ||||||||||
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Big Data Processor Resource Report Resource Website 1+ mentions |
Big Data Processor (RRID:SCR_018484) | BDP | data processing software, image analysis software, image processing software, software application, software resource | Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy. | Image, image processor, data processor, data, processing, analysis, image data, microscopy | is a plug in for: Fiji | Free, Available for download, Freely available | https://github.com/embl-cba/fiji-plugin-bigDataProcessor | SCR_018484 | 2026-09-12 12:59:01 | 2 | ||||||||
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Harmony Resource Report Resource Website 10+ mentions |
Harmony (RRID:SCR_018809) | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems. | Imaging, analysis, cellular phenotype quantification, PerkinElmer, high content, screening system, cell phenotypic screening, live cell imaging, | is related to: Perkin Elmer: Operetta CLS | Restricted | SCR_018809 | Harmony 4.8 | 2026-09-12 12:59:06 | 34 | |||||||||
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RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, data processing software, software application, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
Berlin Institute for Medical Systems Biology ; NIGMS R01 GM104962 |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-09-12 12:59:06 | 8 | ||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-09-12 12:59:08 | 4 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-09-12 12:59:08 | 1 | ||||||||
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TwoSampleMR Resource Report Resource Website 500+ mentions |
TwoSampleMR (RRID:SCR_019010) | data analysis software, data processing software, software application, software resource | Software R package for performing Mendelian randomization using genome wide association study summary data. | GWAS data, genome wide associated study data, genome data, Mendelian randomization, analysis | PMID:29846171 | Free, Available for download, Freely available | SCR_019010 | 2026-09-12 12:59:08 | 732 | ||||||||||
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Anvi'o Resource Report Resource Website 10+ mentions |
Anvi'o (RRID:SCR_021802) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities. | analysis, visualization, integrated omics, metagenomics, pangenomics, phylogenomics, microbial omics | Alfred P. Sloan Foundation ; Helmholtz Institute for Functional Marine Biodiversity ; Marine Biological Laboratory ; Simons Foundation ; University of Chicago ; W. M. Keck Foundation |
Free, Available for download, Freely available | biotools:anvio | https://github.com/merenlab/anvio, https://bio.tools/anvio | SCR_021802 | Anvi’o | 2026-09-12 01:00:01 | 21 | |||||||
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LYSIS Resource Report Resource Website 50+ mentions |
LYSIS (RRID:SCR_001385) | LYSIS | data analysis software, data processing software, simulation software, software application, software resource, software toolkit, source code | Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x | modeling, data analysis, system modeling, analysis, nonlinear, principal dynamic modes, nonlinear modeling, windows, matlab | has parent organization: Biomedical Simulations Resource | NIBIB P41-EB001978; NCRR P41-RR01861 |
Free, Freely Available | nlx_152571 | SCR_001385 | 2026-09-12 01:00:07 | 56 | |||||||
|
NeuroExplorer Resource Report Resource Website 1000+ mentions |
NeuroExplorer (RRID:SCR_001818) | NeuroExplorer | commercial organization, data analysis software, data processing software, software application, software resource | Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project | neurophysiology, spike train, spike, statistical test, analysis, windows, mac, 3d data, animation, burst analysis, channel, cross correlogram, electrophysiology, matlab, raster analysis, scripting | is listed by: 3DVC | Free, Available for download, Freely available | nlx_158483, nif-0000-10382 | http://www.plexon.com/products/neuroexplorer | SCR_001818 | NeuroExplorer: Neurophysiological Data Analysis Package | 2026-09-12 01:00:07 | 1297 | ||||||
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Neuronland: NLMorphologyConverter Resource Report Resource Website 1+ mentions |
Neuronland: NLMorphologyConverter (RRID:SCR_001817) | data analysis software, data processing software, data visualization software, rendering software, simulation software, software application, software resource | NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand. | format, generation, analysis, biological, morphology, neuron, reconstruction, simulation, three-dimensional, visualization | Free, Available for download, Freely available | nif-0000-10381 | SCR_001817 | NLMorphologyConverter | 2026-09-12 01:00:07 | 8 | |||||||||
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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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Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) Resource Report Resource Website 50+ mentions |
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) | AMP T2D, T2DKP | data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal | Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease. | type 2 diabetes, diabetes, knowledge, portal, database, repository, type II, diabetic, genetic, data, analysis, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Consortia-pedia is listed by: NIDDK Information Network (dkNET) is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus is related to: Type 1 Diabetes Knowledge Portal is related to: Common Metabolic Diseases Knowledge Portal has parent organization: Foundation for the National Institutes of Health has parent organization: Accelerating Medicines Partnership |
Type 2 diabetes, Diabetes | Broad Institute ; Fundacion Carlos Slim ; NIDDK ; NIH ; University of Michigan |
Free, Freely available | SCR_014533, nlx_157976 | http://www.nih.gov/science/amp/type2diabetes.htm | SCR_003743 | , AMP Diabetes, AMP, T2D, AMP-T2D, Type 2 Diabetes Knowledge Portal, Accelerating Medicines Partnership Type 2 Diabetes, Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, The AMP-T2D Knowledge Portal, AMP T2D, AMP Type 2 Diabetes | 2026-09-12 01:00:09 | 83 | ||||
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University of Bergen Computational Biology Unit Resource Report Resource Website 1+ mentions |
University of Bergen Computational Biology Unit (RRID:SCR_002970) | UiB CBU | data or information resource, department portal, organization portal, portal | An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses. | computational, biology, bioinformatics, analysis, structure, molecular, evolution, genome, annotation, functional genomic, programming, rna, dna, molecular biology, protein modelling, integrated genomics, evolutionary genomics | has parent organization: University of Bergen; Bergen; Norway | Research Council of Norway ; FUGE programme |
nif-0000-30147 | http://www.cbu.uib.no | SCR_002970 | UiB Computational Biology Unit | 2026-09-12 01:00:09 | 1 | ||||||
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MetaMorph Microscopy Automation and Image Analysis Software Resource Report Resource Website 5000+ mentions |
MetaMorph Microscopy Automation and Image Analysis Software (RRID:SCR_002368) | MetaMorph | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression. | automated, microscope, acquisition, device, control, image, analysis, fluorescent, cell, signaling, counting, protein, expression, Molecular Devices | PMID:18367250 | Commercially available | SciRes_000136 | SCR_002368 | MetaMorph version 7.8.0.0, Molecular Devices Metamorph Premier Software, MetaMorph image analysis software, MetaMorph Microscopy Automation and Image Analysis Software | 2026-09-12 01:00:08 | 8382 | |||||||
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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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CalR Resource Report Resource Website 100+ mentions |
CalR (RRID:SCR_015849) | data analysis software, data processing software, data visualization software, software application, software resource, web application | A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates. | indirect, calorimerty, analysis, visualization, energy, balance, food intake, energy expenditure, metabolism, metabolic phenotyping, CLAMS, PhenoMaster, Prometheon, biostatistics, ANCOVA, reproducibility, Columbus Instruments, Sable Systems, TSE | is related to: Harvard University; Cambridge; United States | Harvard Digestive Disease Center ; Mouse Metabolic Phenotyping Center ; NIDDK |
DOI:10.1101/213967 | Freely available, Public | https://calrapp.org | SCR_015849 | A Web Application for Indirect Calorimetry Analysis | 2026-09-12 12:58:31 | 228 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
