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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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iMITS Resource Report Resource Website |
iMITS (RRID:SCR_016552) | iMITS | data or information resource, catalog, database | This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products. | international, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPC |
is affiliated with: International Mouse Phenotyping Consortium (IMPC) is related to: GenTaR |
NIH KOMP2; European Union 223592 |
Restricted | SCR_016552 | international Micro Injection Tracking System | 2026-02-17 10:03:02 | 0 | |||||||
|
Suite2P Resource Report Resource Website 50+ mentions |
Suite2P (RRID:SCR_016434) | software application, image processing software, data processing software, data analysis software, software resource, 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 | 2026-02-17 10:03:01 | 71 | ||||||||||
|
MotionCor2 Resource Report Resource Website 100+ mentions |
MotionCor2 (RRID:SCR_016499) | data analysis software, software application, data processing software, software resource | 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 | 2026-02-17 10:03:25 | 172 | ||||||
|
Image Pro Resource Report Resource Website 500+ mentions |
Image Pro (RRID:SCR_016497) | software application, image processing software, data processing software, software resource, 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 | 2026-02-17 10:03:27 | 540 | ||||||||
|
Human Cell Atlas Resource Report Resource Website 50+ mentions |
Human Cell Atlas (RRID:SCR_016530) | data or information resource, catalog, map, atlas, database, 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 | 2026-02-17 10:03:27 | 97 | |||||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | software application, data processing software, data analysis software, software resource, 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 | 2026-02-17 10:03:01 | 5 | |||||||
|
Cardiovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) | data or information resource, topical portal, disease-related portal, database, 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 | 2026-02-17 10:03:02 | 28 | ||||||||
|
VoxBlast Resource Report Resource Website 1+ mentions |
VoxBlast (RRID:SCR_016491) | 3d visualization software, software application, image processing software, data processing software, software resource, data 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 | 2026-02-17 10:02:42 | 1 | ||||||||||
|
OMA Orthology database Resource Report Resource Website 1+ mentions |
OMA Orthology database (RRID:SCR_016425) | OMA | data access protocol, software application, standalone software, data or information resource, database, software resource, web service | 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 | 2026-02-17 10:02:42 | 9 | |||||||
|
HARP Resource Report Resource Website |
HARP (RRID:SCR_016546) | 3d visualization software, software application, image processing software, standalone software, data processing software, software resource, data visualization 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 | 2026-02-17 10:03:25 | 0 | |||||||||
|
kCSD-Matlab Resource Report Resource Website 1+ mentions |
kCSD-Matlab (RRID:SCR_016424) | kCSD | data analysis software, software application, data processing software, software resource | 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 | 2026-02-17 10:03:24 | 2 | ||||||||
|
BIOQUANT Life Science Resource Report Resource Website 10+ mentions |
BIOQUANT Life Science (RRID:SCR_016423) | software application, data processing software, data analysis software, software resource, software toolkit, image analysis software | 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 | 2026-02-17 10:03:01 | 19 | |||||||||||
|
CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | data or information resource, database, 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 | 2026-02-17 10:03:02 | 1 | ||||||||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | software application, web application, data processing software, data analysis software, software resource, sequence analysis 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 | 2026-02-17 10:03:27 | 4 | ||||
|
Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | software application, data processing software, data analysis software, software resource, software toolkit, data visualization software | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Research Foundation SFB 992; German Epigenome Programme DEEP 01KU1216G |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-02-17 10:03:24 | 2418 | |||||||
|
PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | software application, data or information resource, source code, database, 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 | 2026-02-17 10:03:25 | 2 | |||||||||
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | software application, data processing software, data analysis software, software resource, 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 | 2026-02-17 10:03:27 | 35 | |||||||||
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SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software application, data processing software, data analysis software, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-02-17 10:03:23 | 2 | |||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | data access protocol, data or information resource, topical portal, project portal, database, software resource, web service, portal, organism-related 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 | 2026-02-17 10:02:42 | 2 | |||||||||
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MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | software application, data processing software, data analysis software, software resource, sequence analysis 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 | 2026-02-17 10:03:27 | 8 |
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