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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications. | annotation, quantification, miRNA, smRNA-seq, data, functionally, distinct, isoform, isomiR, quality, sequencing, genome, mapping, statistic, tDR, yDR | PMID:28187421 | Free, Available for download, Freely available | SCR_017261 | miRquant 2.0 | 2026-08-29 11:25:32 | 1 | |||||||||
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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 | 2026-08-29 11:25:26 | 2 | ||||||||
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Diffusion Toolkit Resource Report Resource Website 50+ mentions |
Diffusion Toolkit (RRID:SCR_017345) | DTK | data analysis software, data processing software, software application, software resource | Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography. | data, reconstruction, fiber, tracking, diffusion, MR, image, processing, tractography |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard University; Cambridge; United States |
Restricted | https://cds.ismrm.org/ismrm-2007/files/03720.pdf, https://www.nitrc.org/projects/trackvis/ | SCR_017345 | 2026-08-29 11:25:59 | 67 | ||||||||
|
PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NHGRI HG005998; NIGMS P50 GM071508; NIGMS R01 GM071966 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-08-29 11:25:37 | 8 | ||||||||
|
TissueAtlas Resource Report Resource Website 10+ mentions |
TissueAtlas (RRID:SCR_017352) | atlas, data access protocol, data or information resource, database, software resource, web service | Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues. | Human, miRNA, tissue, atlas, data, distribution, expression | has parent organization: Saarland University; Saarbrucken; Germany | FP7 project BestAgeing ; Saarland University ; Germany ; Siemens Healthcare |
PMID:26921406 | Free, Freely available | SCR_017352 | 2026-08-29 11:25:59 | 37 | ||||||||
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clusterExperiment Resource Report Resource Website |
clusterExperiment (RRID:SCR_017439) | data analysis software, data processing software, data visualization software, software application, software resource | Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data. | Executing, evaluating, visualizing, clustering, experimental, data, single, cell, RNAseq, sequencing, gene, expression, BRAIN Initiative | is recommended by: BRAIN Initiative | Chan Zuckerberg Initiative ; ENS-CFM Data Science Chair ; NIMH U01 MH105979; NIMH U19 MH114830 |
PMID:30180157 | Free, Available for download, Freely available | SCR_017439 | 2026-08-29 11:25:40 | 0 | ||||||||
|
HmtPhenome Resource Report Resource Website |
HmtPhenome (RRID:SCR_017289) | data or information resource, data processing software, data visualization software, database, network graph visualization software, service resource, software application, software resource | Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality. Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities. | mitochondria, variant, gene, function, phenotype, data |
uses: Human Phenotype Ontology uses: Ensembl uses: OMIM uses: Orphanet uses: DisGeNET has parent organization: University of Bari; Bari; Italy |
DOI:10.1101/660282 | Free, Freely available | SCR_017289 | 2026-08-29 11:25:58 | 0 | |||||||||
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Tissue Mapper Resource Report Resource Website 1+ mentions |
Tissue Mapper (RRID:SCR_017321) | 3d visualization software, data processing software, data visualization software, image analysis software, image reconstruction software, segmentation software, software application, software resource | Software for comprehensive annotation and delineation of tissue structures by MBF Bioscience. Creates 3D model from image data and annotates regions of interest from customizable ontology list. Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes. | MBF Bioscience, annotation, delineation, mapping, 3D model, image, data, tissue, structure | is used by: SPARC Portal | Restricted | SCR_017321 | Tissue MapperTM, Tissue Mapper | 2026-08-29 11:25:58 | 4 | |||||||||
|
Relacs Resource Report Resource Website 1+ mentions |
Relacs (RRID:SCR_017280) | data acquisition software, data analysis software, data processing software, software application, software resource | Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings. | data, acquisition, analysis, electrophysiology, neuronal, response, control, stimulation | Free, Available for download, Freely available | SCR_017280 | Control, and Stimulation, Relaxed Electrophysiological Data Acquisition | 2026-08-29 11:25:58 | 2 | ||||||||||
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Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | 3d visualization software, data analysis software, data processing software, data visualization software, image analysis software, segmentation software, software application, software resource | Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience. | MBF Bioscience, vasculature, reconstruction, image, analysis, 3D, vessel, data, automatic, quantify, anastomoses, microvascular |
is used by: SPARC Portal works with: Vesselucida Explorer |
Restrcited | https://learn.mbfbioscience.com/vle.html | SCR_017320 | Vesselucida 360, Vesselucida | 2026-08-29 11:25:35 | 2 | |||||||
|
BioWheel Resource Report Resource Website |
BioWheel (RRID:SCR_017441) | data processing software, data visualization software, software application, software resource | Software tool for interactive graphs of high dimensional data. Interactive cloud based software tool by DIBSVIS. | Interactive, graph, high, dimensional, data, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Restricted | SCR_017441 | , bio wheel, biowheel | 2026-08-29 11:25:35 | 0 | ||||||||
|
NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | alignment software, data processing software, image analysis software, software application, software resource | Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data. | de novo, assembler, heteroplasmy, variance, caller, short, circular, genome, organelle, whole, data | is listed by: OMICtools | Belgian Kids Fund ; Hôpital Universitaire des Enfants Reine Fabiola ; Interuniversity Institute of Bioinformatics in Brussels |
PMID:28204566 | Free, Available for download, Freely available | SCR_017335 | 2026-08-29 11:25:59 | 202 | ||||||||
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Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data or information resource, data processing software, software application, software resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind | SCR_017339 | 2026-08-29 11:25:36 | 1 | |||||||||
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MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | data analysis software, data processing software, software application, software resource | Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab. | post, process, magnetic, resonance, spectroscopy, data, analysis |
has parent organization: University of Minnesota Twin Cities; Minnesota; USA works with: MATLAB |
Restricted | SCR_017292 | Magnetic Resonance signal processing and analysis | 2026-08-29 11:25:34 | 19 | |||||||||
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Kinetic Models of Biological Systems (KiMoSys) Resource Report Resource Website 1+ mentions |
Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) | data access protocol, data repository, service resource, software resource, storage service resource, web service | Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community. | Quantitative, kinetic, model, biological, system, data, storage, search, exchange, experiment |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
EU ; Portuguese national funding agency for science ; research and technology. |
Restricted | r3d100011562 | https://doi.org/10.17616/R3864V | https://fairsharing.org/FAIRsharing.6erywc | SCR_017423 | , Kinetic Models of Biological Systems (KiMoSys), KInetic MOdels of biological SYStems, KiMoSys | 2026-08-29 11:25:39 | 1 | |||||
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | data analysis software, data processing software, data visualization software, software application, software resource | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Victorian State Government Operational Infrastructure Support and Australian Government ; Viertel Fellowship |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-08-29 11:25:38 | 23 | ||||||||
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HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R. | homoplasy, phylogeny, sequence, alignment, identify, data, annotate | Science Foundation Ireland | PMID:30663960 | Free, Available for download, Freely available | https://github.com/JosephCrispell/homoplasyFinder | SCR_017300 | 2026-08-29 11:25:34 | 6 | ||||||||
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The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data. | Multivariate, analysis, structural, MRI, data, functional, imaging, brain | German Ministry of Education and Research ; German Research Foundation |
PMID:25610393 | Free, Available for download, Freely available | SCR_017424 | 2026-08-29 11:26:00 | 16 | ||||||||
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Inorganic Crystal Structure Database (ICSD) Resource Report Resource Website 10+ mentions |
Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) | ICSD | data or information resource, data repository, database, service resource, storage service resource | Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research. | Inorganic, crystal, structure, data, atomic, coordinate, quality, FIZ Karlsruhe — Leibniz Institute for Information Infrastructure |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Restricted | r3d100010085 | http://www2.fiz-karlsruhe.de/icsd_home.html, https://doi.org/10.17616/R3GW2V | SCR_017429 | Inorganic Crystal Structure Database, Inorganic Crystal Structure Database (ICSD), ICSD | 2026-08-29 11:25:40 | 11 | ||||||
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SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-08-29 11:25:33 | 2 |
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