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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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VoxBlast Resource Report Resource Website 1+ mentions |
VoxBlast (RRID:SCR_016491) | image processing software, data processing software, software application, software resource, data visualization 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 | 2026-08-14 09:27:35 | 1 | ||||||||||
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nonparametricGGC_toolbox Resource Report Resource Website 1+ mentions |
nonparametricGGC_toolbox (RRID:SCR_016539) | nonparametricGGC | data processing software, software application, data analysis software, software resource | Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions. | nonparametric, Granger, causality, simulation, framework, code, estimate, brain, function | is related to: MATLAB | the Swiss National Science Foundation | Free, Available for download, Freely available | SCR_016539 | nonparametric Granger Geweke Causality | 2026-08-14 09:27:45 | 2 | |||||||
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findMotif.pl Resource Report Resource Website 1+ mentions |
findMotif.pl (RRID:SCR_016417) | software toolkit, data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool to analyze the promoters of genes and look for motifs that are enriched in the target gene promoters relative to other promoters. Used for gene based analysis to provide a list of genes that should contain the same elements, such as genes that are co-regulated. It includes gene ontology analysis and can be used to look for RNA motifs in mRNAs. | analyze, promoter, gene, motif, target, relative, same, element, ontology, RNA, mRNA |
is related to: HOMER has parent organization: University of California at San Diego; California; USA |
Free, Available for download, Freely available | SCR_016417 | 2026-08-14 09:27:24 | 4 | ||||||||||
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OMA Orthology database Resource Report Resource Website 1+ mentions |
OMA Orthology database (RRID:SCR_016425) | OMA | database, standalone software, web service, data or information resource, data access protocol, software application, software resource | 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 | 2026-08-14 09:27:34 | 9 | |||||||
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HARP Resource Report Resource Website 1+ mentions |
HARP (RRID:SCR_016546) | standalone software, image processing software, data processing software, software application, software resource, data visualization software, 3d 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 | 2026-08-14 09:27:45 | 1 | |||||||||
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kCSD-Matlab Resource Report Resource Website 1+ mentions |
kCSD-Matlab (RRID:SCR_016424) | kCSD | data processing software, software application, data analysis 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 | 2026-08-14 09:27:42 | 3 | ||||||||
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VPV Resource Report Resource Website 1+ mentions |
VPV (RRID:SCR_016545) | VPV | data processing software, software application, software resource, data visualization software, 3d visualization software | Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph. | Phyton, desktop, 3D viewer, analysis, results, phenotype, detection, LAMA pipeline | is listed by: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | SCR_016545 | Volume Phenotype Viewer, volume phenotype viewer | 2026-08-14 09:27:26 | 1 | ||||||||
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BIOQUANT Life Science Resource Report Resource Website 10+ mentions |
BIOQUANT Life Science (RRID:SCR_016423) | software toolkit, image analysis software, data processing software, software application, data analysis software, software resource | 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 | 2026-08-14 09:27:24 | 20 | |||||||||||
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DCC Resource Report Resource Website 1+ mentions |
DCC (RRID:SCR_016544) | DCC | data processing software, software application, data analysis software, software resource | Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts. | databases, sequencing experiments, sequencing annotation, data annotation | Free, Available for download, Freely available | SCR_016544 | Data Coordination Center | 2026-08-14 09:27:35 | 1 | |||||||||
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RNA22 Resource Report Resource Website 100+ mentions |
RNA22 (RRID:SCR_016507) | RNA22 | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases. | pattern, based, detecting, microRNA, binding, site, complex, sequence, genome, analysis, FASEB list | is listed by: OMICtools | A Star ; Singapore ; NIDDK DK04763; NIH AI54973 |
Free, Available for download, Freely available | SCR_016507 | RiboNucleic Acid 22 | 2026-08-14 09:27:35 | 222 | |||||||
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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 | 2026-08-14 09:27:45 | 1 | ||||||||||
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data processing software, web application, software application, 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 | 2026-08-14 09:27:25 | 6 | ||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | data processing software, software application, data analysis software, data analytics software, software resource, sequence analysis software | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 355804783; Wellcome Trust WT092340; Wellcome Trust WT083481; Wellcome Trust 106370Z14 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | Jprotein secondary structure PREDiction | 2026-08-14 09:27:35 | 133 | ||||||||
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miRmap Resource Report Resource Website 100+ mentions |
miRmap (RRID:SCR_016508) | software toolkit, software application, data analytics software, software resource, software library | Software application as an open source Pyton library to search and predict miRNA targets. | search, predict, miRNA, target | is listed by: OMICtools | Swiss National Science Foundation ; Swiss Institute of Bioinformatics |
PMID:23034802 | Free, Available for download, Freely available, Tutorial available | http://cegg.unige.ch/mirmap | SCR_016508 | 2026-08-14 09:27:25 | 227 | |||||||
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PhenoSpD Resource Report Resource Website 1+ mentions |
PhenoSpD (RRID:SCR_016359) | PSD | software toolkit, data processing software, software application, data analysis software, software resource | Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool. | spectral, decomposition, matrice, phenotypic, correlation, estimation, multiple, testing, correction, human, phenome, genome, summary, statistic, decomposition, matrice, genomics |
is related to: University of Bristol; Bristol; United Kingdom is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016359 | Pheno Spectral Decomposition, PhenoSpD | 2026-08-14 09:27:41 | 6 | ||||||||
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NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | data processing software, web application, software application, data analysis software, software resource, sequence analysis software | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2026-08-14 09:27:34 | 1 | |||||||
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MetaPGN Resource Report Resource Website 1+ mentions |
MetaPGN (RRID:SCR_016472) | MetaPGN | software toolkit, data processing software, software application, data analysis software, network graph visualization software, software resource, data visualization software | Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | construct, graphical, visualization, annotated, pangenome, network, microbal, genome, metagenome | PMID:30277499 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/peng-ye/MetaPGN | SCR_016472 | Meta PanGeNome | 2026-08-14 09:27:44 | 2 | |||||||
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Thermo Fisher: Nanodrop 1000 Spectrophotometer Resource Report Resource Website 50+ mentions |
Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) | instrument resource | Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution. | ABRF, spectrophotometer, nanodrop, concentration measurement, optical density, DNA, RNA, protein, nanodrop, instrument, equipment |
is listed by: USEDit works with: Thermo Scientific NanoDrop 1000 Software |
Commercially available | https://drive.google.com/file/d/1C1Dj_A1QxQibucCbFNues9EDZebDnx8K/view?usp=drivesdk | SCR_018035, Model_Number_Nanodrop_1000, SCR_020560 | https://www.marshallscientific.com/Nanodrop-ND-1000-Spectrophotometer-p/nd-1000.htm, https://www.selectscience.net/products/nanodrop-1000-spectrophotometer/?prodID=79482#tab-2, http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf | SCR_016517 | NanoDrop 1000, Nanodrop ND-1000, Thermo Scientific NanoDrop 1000, NanoDrop 1000 Spectrophotometer | 2026-08-14 09:27:25 | 89 | ||||||
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Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | software toolkit, data processing software, software application, data analysis software, software resource, 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 | 2026-08-14 09:27:42 | 2806 | |||||||
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PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | database, data or information resource, software application, 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 | 2026-08-14 09:27:44 | 2 |
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