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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Suite2P Resource Report Resource Website 50+ mentions |
Suite2P (RRID:SCR_016434) | software application, data analysis software, software resource, data processing software, image processing software, software toolkit | Software package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. | two, photon, microscopy, processing, image, data, record |
is related to: MATLAB has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | SCR_016434 | 2026-07-28 09:44:17 | 71 | ||||||||||
|
SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | software application, data analysis software, software resource, data processing software, data analytics software | Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis. | single, cell, RNA seq, data, sorted, whole, organ, profiling, analysis | NHLBI U01 HL110964; NHLBI U01 HL122642; NHLBI R01 HL105433 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-07-28 09:44:21 | 5 | ||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | software application, data analysis software, software resource, data processing software, data visualization software, image processing software, standalone software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | MIB, Microscopy Image Browser | 2026-07-28 09:44:21 | 143 | ||||
|
MotionCor2 Resource Report Resource Website 100+ mentions |
MotionCor2 (RRID:SCR_016499) | software application, software resource, data analysis software, data processing software | Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux. | anisotropic, correction, beam, induced, motion, cryo, electron, microscopy, exposure, data | has parent organization: University of California at San Francisco; California; USA | NIH R01 GM031627; NIGMS P01 GM111126 |
PMID:28250466 | Restricted | http://msg.ucsf.edu/em/software/motioncor2.html | SCR_016499 | MotionCor | 2026-07-28 09:44:20 | 172 | ||||||
|
Image Pro Resource Report Resource Website 500+ mentions |
Image Pro (RRID:SCR_016497) | software application, software resource, data processing software, image processing software, image analysis software | Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection. | MediaCybernetics Inc., capture, process, measure, analyze, share, image, data, automate, collect | Restricted | SCR_016758 | https://mediacy.com/image-pro | SCR_016497 | Image-Pro, Image-Pro Premier, Image Pro Premier | 2026-07-28 09:44:15 | 540 | ||||||||
|
Human Cell Atlas Resource Report Resource Website 50+ mentions |
Human Cell Atlas (RRID:SCR_016530) | map, data or information resource, catalog, database, atlas, image, portal | Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease. | human, cell, line, atlas, catalog, map, open, data, international, project, FASEB list |
is listed by: NIDDK Information Network (dkNET) is related to: Optimus Pipeline is related to: Smart-seq2 Multi-Sample Pipeline is related to: Broad Institute Genomics Platform |
PMID:29206104 | Free, Available for download, Freely available | SCR_016530 | 2026-07-28 09:44:20 | 97 | |||||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | software application, data analysis software, software resource, data processing software, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-07-28 09:44:18 | 5 | |||||||
|
Cardiovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) | disease-related portal, data or information resource, database, topical portal, portal | Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data. | genetic, data, cardiovascular, disease, human | is listed by: NIDDK Information Network (dkNET) | cardiovascular disease, myocardial infarction, atrial fibrillation | Accelerating Medicines Partnership in Type 2 Diabetes ; National Institute of Cardiovascular Diseases and Stroke |
Free, Available for download, Google ID required, Tutorial available | SCR_016536 | 2026-07-28 09:44:20 | 28 | ||||||||
|
VoxBlast Resource Report Resource Website 1+ mentions |
VoxBlast (RRID:SCR_016491) | software application, software resource, data processing software, data visualization software, image processing software, 3d visualization software | Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint. | VayTek Inc., 3D, image, data, visualisation, reconstruction, measurement, projection, science, medicine |
is listed by: OMICtools has parent organization: University of Iowa Labs and Facilities |
Commercially available, Free demo version available | SCR_016491 | 2026-07-28 09:44:19 | 1 | ||||||||||
|
OMA Orthology database Resource Report Resource Website 1+ mentions |
OMA Orthology database (RRID:SCR_016425) | OMA | software application, data or information resource, database, data access protocol, software resource, web service, standalone software | Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | interface, orthology, prediction, inference, complete, genome, species, data | Swiss Institute of Bioinformatics ; UK Biotechnology and Biological Sciences Research Council ; University College London ; Bayer Crop Science NV |
PMID:29106550 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016425 | Orthologous MAtrix | 2026-07-28 09:44:17 | 9 | |||||||
|
HARP Resource Report Resource Website |
HARP (RRID:SCR_016546) | software application, software resource, data processing software, data visualization software, image processing software, 3d visualization software, standalone software | Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release. | MRC Harwell UK, automating, processing, uCT, OPT, image, data | is related to: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | harp.exe | SCR_016546 | 2026-07-28 09:44:20 | 0 | |||||||||
|
kCSD-Matlab Resource Report Resource Website 1+ mentions |
kCSD-Matlab (RRID:SCR_016424) | kCSD | software application, software resource, data analysis software, data processing software | Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes. | analyzing, recording, data, multielectrode, transmembrane, current, source, estimate, kernel, source, density, method | is related to: MATLAB | Free, Available for download, Freely available | SCR_016424 | kernel Current Source Density | 2026-07-28 09:44:13 | 2 | ||||||||
|
BIOQUANT Life Science Resource Report Resource Website 10+ mentions |
BIOQUANT Life Science (RRID:SCR_016423) | software application, image analysis software, data analysis software, software resource, data processing software, software toolkit | Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders. | BioQuant Inc., collect, analyse, data, tissue, slide, well, plate, capture, camera, scanned, image, immunofluorescence, immunohistochemistry, stereology, densitometry, 3D modeling | Commercially available, Tutoring available | SCR_016423 | 2026-07-28 09:44:18 | 19 | |||||||||||
|
CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | database, data or information resource, web application, software resource | Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network. | marmoset, data, genomic, expression, alternative, splicing, animal, model, neuropsychiatry, social, behavior, ontology, protein, network | Amazonas State Research Support Foundation ; Federal University of Rio Grande do Norte ; Brain Institute ; Multidisciplinary Environment ; NPAD/UFRN ; Brazilian Council for Research and Technological Development |
Free, Freely available | SCR_016506 | 2026-07-28 09:44:16 | 1 | ||||||||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | software application, web application, data analysis software, sequence analysis software, software resource, data processing software | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-07-28 09:44:20 | 4 | ||||
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PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | software application, data or information resource, database, source code, software resource | Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective". | data, code, Phyton, research, paper, probabilistic, neural, network | Free, Available for download, Freely available | SCR_016485 | Probabilistic Neural Networks MiceMachineVision | 2026-07-28 09:44:15 | 2 | |||||||||
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | software application, data analysis software, software resource, data processing software, software toolkit | Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. | geometric, morphometric, analyse, 2D, 3D, landmark, data, principal, component, discriminant, multivariate, regression, shape | has parent organization: University of Manchester; Manchester; United Kingdom | PMID:21429143 | Free, Available for download, Freely available | SCR_016483 | 2026-07-28 09:44:19 | 35 | |||||||||
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SABRe CVD Initiative Resource Report Resource Website |
SABRe CVD Initiative (RRID:SCR_016572) | SABRe CVD | disease-related portal, data or information resource, topical portal, portal | Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation. | generate, biomarker, discovery, data, Framingham, Heart, Study, gene, expression, omicdata | cardiovascular disease, atherosclerosis | Free, Partially available for public, Requested authorized access | SCR_016572 | Systems Approach to Biomarker Research in CardioVascular Disease | 2026-07-28 09:44:21 | 0 | ||||||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | data or information resource, project portal, organism-related portal, database, data access protocol, software resource, web service, topical portal, portal | Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. | project, genomic, information, fungi, data, sequence, energy, environment |
is related to: MycoCosm is related to: Lawrence Berkeley National Laboratory has parent organization: DOE Joint Genome Institute |
the DOE Office of Biological and Environmental Research (BER) | Free, Register for an account | SCR_016463 | 2026-07-28 09:44:19 | 2 | |||||||||
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MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-07-28 09:44:18 | 8 |
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