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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | data processing software, 3d visualization software, data analysis software, segmentation software, data visualization software, software resource, image analysis 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 | 2026-07-30 09:30:18 | 2 | |||||||
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NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | data processing software, software resource, image analysis software, alignment 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 | 2026-07-30 09:30:13 | 161 | ||||||||
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University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility Resource Report Resource Website |
University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility (RRID:SCR_017179) | UM School of Medicine Computational Medicine and Bioinformatics, CCMB, Center of Computational Medicine and Bioinformatics | core facility, data or information resource, service resource, access service resource | University interdisciplinary academic center for bioinformatics, biomedical data science, and translational precision health informatics. Core provides training programs. | Bioinformatics, biomedical, data, translational, informatics | Restricted | SCR_017179 | University of Michigan, CCMB, Computational Medicine and Bioinformatics, UM, School of Medicine | 2026-07-30 09:30:07 | 0 | |||||||||
|
IBM® MarketScan® Research Databases Resource Report Resource Website 10+ mentions |
IBM® MarketScan® Research Databases (RRID:SCR_017212) | data or information resource, database, data set | 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 | 2026-07-30 09:30:07 | 37 | |||||||||||
|
Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data or information resource, software resource, software application, data processing software | 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 | 2026-07-30 09:30:09 | 1 | |||||||||
|
CytExpert Software Resource Report Resource Website 500+ mentions |
CytExpert Software (RRID:SCR_017217) | data processing software, data analysis software, software resource, software application, data acquisition software | 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 | 2026-07-30 09:30:07 | 888 | |||||||||
|
PennAI Resource Report Resource Website |
PennAI (RRID:SCR_017215) | data processing software, data management software, data analysis software, data visualization software, software resource, 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 | 2026-07-30 09:30:17 | 0 | ||||||||
|
MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | data processing software, software application, data analysis software, 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 | 2026-07-30 09:30:08 | 19 | |||||||||
|
Montreal Clinical Research Bioinformatics Core Facility Resource Report Resource Website |
Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) | IRCM BIF, BIF | core facility, service resource, access service resource, training service resource, data analysis service, data or information resource, production service resource, analysis service resource | Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses. | bioinformatics, genomic, omics, data, analysis, RNA-Seq, CHIP-Seq, RIP-Seq, DNA, methylation, DNA-Seq, rRNA, microarray | Restricted | SCR_017176 | , Institute of Clinical Research of Montreal, IRCM, Bioinformatics Core Facility, BIF | 2026-07-30 09:30:07 | 0 | |||||||||
|
FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | service resource, data access protocol, software resource, web service, production service resource, 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 | 2026-07-30 09:30:12 | 20 | |||||||
|
HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | data processing software, software toolkit, data analysis software, software resource, standalone 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 | 2026-07-30 09:30:08 | 4 | ||||||||
|
miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | data processing software, data analytics software, data analysis software, software resource, 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 | 2026-07-30 09:30:18 | 1 | |||||||||
|
SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | data processing software, sequence analysis software, data analysis software, software resource, software application | 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 | 2026-07-30 09:30:18 | 2 | |||||||||
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QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | data processing software, software application, data analysis software, software resource | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-07-30 09:30:18 | 28 | |||||||||||
|
SCÅTTER Resource Report Resource Website 50+ mentions |
SCÅTTER (RRID:SCR_017271) | service resource, data access protocol, software resource, web service, production service resource, analysis service resource | Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets. | analysis, data, dataset, small, angle, X ray, scattering, SAXS, BIOISIS | Department of Energy Office of Science Integrated Diffraction Analysis Technologies ; National Cancer Institute Structural Cell Biology of DNA Repair Machines ; National Institute of General Medical Sciences project MINOS |
Restricted | https://bl1231.als.lbl.gov/scatter/ | SCR_017271 | 2026-07-30 09:30:18 | 84 | |||||||||
|
4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | service resource, data repository, data or information resource, database, storage service resource | Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community. | Repository, chromatic, interaction, data, genomic, region, gene, name, detection, technology, curated | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | r3d100012282 | https://doi.org/10.17616/R3SH37 | SCR_017489 | 2026-07-30 09:30:21 | 10 | ||||||||
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National Twin Registry of Sri Lanka Resource Report Resource Website |
National Twin Registry of Sri Lanka (RRID:SCR_017481) | NTR | service resource, data repository, data or information resource, database, storage service resource | Independent academic and research institution to establish registration for twins in Sri Lanka , to facilitate study of twins. Center for twin, sibling, family and genetic studies for South Asian Region. | Registration, twin, data, repository, genetics, South Asian Region | Wellcome Trust UK | https://www.ird.lk/ | SCR_017481 | Sri Lankan Twin Registry | 2026-07-30 09:30:21 | 0 | ||||||||
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Virginia Commonwealth University Mid-Atlantic Twin Registry MATR Core Facility Resource Report Resource Website |
Virginia Commonwealth University Mid-Atlantic Twin Registry MATR Core Facility (RRID:SCR_017484) | core facility, data or information resource, service resource, access service resource | Core scientists collaborate with research teams from a variety of disciplines and institutions. MATR services include recruitment, data and sample collection, dataset curation and access, protocol development, cost estimates, grant development support, and IRB submissions. Twins and their families who are willing to consider taking part in twin-based, health-related research can participate. For twins of any age, ethnicity, and zygosity (identical or fraternal), as well as higher order multiples such as triplets, quadruplets and quintuplets. Most of twins registered in MATR are from Virginia, North Carolina, and South Carolina, but twins from all over the country and all around the world are welcome to register. MATR repository containing DNA samples provided by twins and allows to study twin data collected by studies along with their DNA. | ABRF, twin, data, repository, DNA, sample, Virginia Commonwealth University, |
is listed by: ABRF CoreMarketplace has parent organization: Virginia Commonwealth University; Virginia; USA |
Open | ABRF_5679 | https://https://coremarketplace.org/?FacilityID=5679&citation=1, https://matr.vcu.edu/ | SCR_017484 | , Mid-Atlantic Twin Registry (MATR), VCU Mid-Atlantic Twin Registry, Virginia Commonwealth University VCU Mid-Atlantic Twin Registry (MATR) | 2026-07-30 09:30:15 | 0 | |||||||
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Accessible Resource for Integrated Epigenomics Studies Resource Report Resource Website 10+ mentions |
Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) | data access protocol, software resource, web service, portal, topical portal, data or information resource | Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time. | Epigenomic, human, tissue, DNA, methylation, data, peripheral, blood | BBSRC ; Medical Research Council ; Wellcome Trust ; University of Bristol |
PMID:25991711 | Free, Freely available | http://www.bristol.ac.uk/alspac/ | SCR_017492 | ARIES | 2026-07-30 09:30:21 | 33 | |||||||
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Deep Blue Epigenomic Data Server Resource Report Resource Website 1+ mentions |
Deep Blue Epigenomic Data Server (RRID:SCR_017490) | service resource, access service resource, data access protocol, software resource, web service, data or information resource | Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis. | Data, epigenomic, collection, ontology, storing, distributing, organizing, retriving, searching, genetic, metadata, analysis |
uses: ENCODE uses: Blueprint Epigenome uses: NIH Roadmap is related to: Roadmap Epigenomics Project |
German Science Ministry ; EU |
Free, Freely available | SCR_017490 | 2026-07-30 09:30:15 | 2 |
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