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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | data analysis software, software application, software resource, data processing software | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-08-06 09:29:00 | 1 | |||||||
|
Diffusion Toolkit Resource Report Resource Website 50+ mentions |
Diffusion Toolkit (RRID:SCR_017345) | DTK | data analysis software, software application, software resource, data processing software | 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 | 2026-08-06 09:29:03 | 55 | ||||||||
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MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, web service, software resource | Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. | real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Waxholm Space |
European Union Horizon 2020 Human brain project | DOI:10.1371/journal.pone.0216796 | Free, Freely available | https://localiview.apps.ebrains.eu/, https://meshview-for-brain-atlases.readthedocs.io, https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases | SCR_017222 | MeshView for brain atlases | 2026-08-06 09:29:00 | 11 | ||||||
|
Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | data analysis software, software application, software resource, data processing software | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | NIH Office of the Director DP2 OD008540; NHLBI U01 HL130010; NSF PHY-1427654; NHGRI HG006193; Welch Foundation ; Cancer Prevention Research Institute of Texas ; NVIDIA Research Center Award ; IBM University Challenge Award ; Google Research Award ; McNair Medical Institute Scholar Award ; President Early Career Award in Science and Engineering ; NHGRI HG003067; PD Soros Fellowship |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-08-06 09:29:00 | 108 | ||||||||
|
PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | 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 |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-08-06 09:29:03 | 7 | ||||||||
|
TissueAtlas Resource Report Resource Website 10+ mentions |
TissueAtlas (RRID:SCR_017352) | software resource, atlas, data access protocol, web service, data or information resource, database | 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 | Saarland University ; Germany ; Siemens Healthcare ; FP7 project BestAgeing |
PMID:26921406 | Free, Freely available | SCR_017352 | 2026-08-06 09:29:03 | 29 | ||||||||
|
HmtPhenome Resource Report Resource Website |
HmtPhenome (RRID:SCR_017289) | network graph visualization software, software resource, service resource, data or information resource, data processing software, data visualization software, software application, database | 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 | 2026-08-06 09:29:01 | 0 | |||||||||
|
Tissue Mapper Resource Report Resource Website 1+ mentions |
Tissue Mapper (RRID:SCR_017321) | software resource, image analysis software, image reconstruction software, 3d visualization software, data processing software, segmentation software, data visualization software, software application | 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 | 2026-08-06 09:29:03 | 4 | |||||||||
|
Relacs Resource Report Resource Website 1+ mentions |
Relacs (RRID:SCR_017280) | data acquisition software, software resource, data analysis software, data processing software, software application | 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 | 2026-08-06 09:29:03 | 2 | ||||||||||
|
Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | software resource, image analysis software, data analysis software, segmentation software, 3d visualization software, data processing software, data visualization software, software application | 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 | 2026-08-06 09:29:02 | 2 | |||||||
|
NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | software resource, image analysis software, alignment software, data processing software, software application | 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 | Interuniversity Institute of Bioinformatics in Brussels ; Belgian Kids Fund ; Hôpital Universitaire des Enfants Reine Fabiola |
PMID:28204566 | Free, Available for download, Freely available | SCR_017335 | 2026-08-06 09:29:02 | 161 | ||||||||
|
IBM® MarketScan® Research Databases Resource Report Resource Website 10+ mentions |
IBM® MarketScan® Research Databases (RRID:SCR_017212) | data set, database, data or information resource | Software suite of proprietary databases that contain one of longest running and largest collection of privately and publicly insured, de identified patient data in USA. Family of data sets that fully integrate many types of data for healthcare research. | Database, dataset, collection, patient, data, healthcare | Available for purchase | SCR_017212 | 2026-08-06 09:29:02 | 37 | |||||||||||
|
Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | software application, data processing software, data or information resource, 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 | 2026-08-06 09:29:03 | 1 | |||||||||
|
CytExpert Software Resource Report Resource Website 500+ mentions |
CytExpert Software (RRID:SCR_017217) | data acquisition software, software resource, data analysis software, data processing software, software application | Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter. | control, instrument, data, collection, analysis, CytoFLEX Platform, Beckman Coulter, flow, cytometry |
is listed by: OMICtools works with: Beckman Coulter: CytoFLEX LX Flow Cytometer |
OMICS_30185 | https://www.beckman.fr/flow-cytometry/instruments/cytoflex/software | SCR_017217 | 2026-08-06 09:29:02 | 888 | |||||||||
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PennAI Resource Report Resource Website |
PennAI (RRID:SCR_017215) | software resource, data analysis software, data management software, data processing software, data visualization software, software application | Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems. | Supervised, machine, learning, technique, data, mining, storing, analysis, visualizationn, artificial, intelligence | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | http://pennai.org/, https://epistasislab.github.io/pennai/ | SCR_017215 | Accessible artificial intelligence from University of Pennsylvania | 2026-08-06 09:29:03 | 0 | ||||||||
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MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | data analysis software, software application, software resource, data processing software | 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 | 2026-08-06 09:29:04 | 19 | |||||||||
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FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data. | computing, theoretical, scattering, profile, structure, fitting, small, angle, X ray, data | has parent organization: University of California at San Francisco; California; USA | Weizmann Institute Advancing Women in Science ; NIGMS R01 GM083960; NCRR U54 RR022220; NIGMS R01 GM105404; Rinat (Pfizer) Inc. ; Lawrence Berkeley National Lab IDAT program ; NIGMS P41 GM109824 |
PMID:23972848 PMID:27151198 |
Free, Available for download, Freely available | SCR_017269 | Fast X-Ray Scattering | 2026-08-06 09:29:04 | 20 | |||||||
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | software resource, data analysis software, data processing software, data visualization software, software application | 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 ; Viertel Fellowship ; Victorian State Government Operational Infrastructure Support and Australian Government |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-08-06 09:29:03 | 23 | ||||||||
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HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | software resource, standalone software, data analysis software, software toolkit, data processing software, software application | 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 | 2026-08-06 09:29:04 | 4 | ||||||||
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miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | software resource, data analytics software, data analysis software, data processing software, software application | 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 | 2026-08-06 09:29:02 | 1 |
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