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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BioWheel Resource Report Resource Website |
BioWheel (RRID:SCR_017441) | software application, data visualization software, data processing software, 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 | 2026-02-15 09:22:05 | 0 | ||||||||
|
NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | software application, data processing software, software resource, alignment software, image analysis software | 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 | 2026-02-15 09:22:03 | 161 | ||||||||
|
Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | software application, data or information resource, data processing software, 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 | 2026-02-15 09:22:03 | 1 | |||||||||
|
MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | software application, data processing software, 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 | 2026-02-15 09:22:00 | 19 | |||||||||
|
FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | software resource, data access protocol, web service, service resource, 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 | 2026-02-15 09:22:01 | 20 | |||||||
|
Kinetic Models of Biological Systems (KiMoSys) Resource Report Resource Website 1+ mentions |
Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) | software resource, data access protocol, web service, service resource, storage service resource, data repository | 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 | 2026-02-15 09:22:04 | 1 | |||||
|
Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | software application, data visualization software, data processing software, software resource, data analysis software | 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 | 2026-02-15 09:22:04 | 23 | ||||||||
|
HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | software application, data processing software, software resource, standalone software, software toolkit, data analysis 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 | 2026-02-15 09:22:02 | 4 | ||||||||
|
The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | software application, data processing software, data analysis software, 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 | 2026-02-15 09:22:02 | 13 | ||||||||
|
miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | software application, data processing software, software resource, data analytics software, data analysis software | 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 | 2026-02-15 09:22:01 | 1 | |||||||||
|
Inorganic Crystal Structure Database (ICSD) Resource Report Resource Website 1+ mentions |
Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) | ICSD | database, service resource, storage service resource, data repository, data or information 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 | 2026-02-15 09:21:20 | 6 | ||||||
|
SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | software application, sequence analysis software, data processing software, software resource, data analysis software | 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 | 2026-02-15 09:22:01 | 2 | |||||||||
|
QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | software application, data processing software, data analysis software, software resource | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-02-15 09:22:02 | 28 | |||||||||||
|
Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | software application, data processing software, software resource, simulation software, data analysis software | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn https://github.com/jonescompneurolab/hnn/tree/0.0.5 https://github.com/jonescompneurolab/hnn/tree/0.1.2 https://zenodo.org/record/2394296#.Xg4rCEdKiM9 https://bio.tools/HNN |
SCR_017437 | 2026-02-15 09:22:04 | 13 | |||||
|
SCÅTTER Resource Report Resource Website 50+ mentions |
SCÅTTER (RRID:SCR_017271) | software resource, data access protocol, web service, service resource, 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 | 2026-02-15 09:21:17 | 84 | |||||||||
|
4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | database, service resource, storage service resource, data repository, data or information 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 | 2026-02-15 09:21:21 | 10 | ||||||||
|
National Twin Registry of Sri Lanka Resource Report Resource Website |
National Twin Registry of Sri Lanka (RRID:SCR_017481) | NTR | database, service resource, storage service resource, data repository, data or information 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 | 2026-02-15 09:22:06 | 0 | ||||||||
|
Mid-Atlantic Twin Registry Resource Report Resource Website |
Mid-Atlantic Twin Registry (RRID:SCR_017484) | MATR | organization portal, portal, service resource, storage service resource, data repository, data or information resource | Organization of twins and their families who are willing to consider taking part in twin-based, health-related research. 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. | Twin, data, repository, DNA, sample, Virginia Commonwealth University | has parent organization: Virginia Commonwealth University; Virginia; USA | Restricted | SCR_017484 | 2026-02-15 09:22:04 | 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) | portal, software resource, data access protocol, web service, data or information resource, topical portal | 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 | 2026-02-15 09:22:03 | 33 | |||||||
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Deep Blue Epigenomic Data Server Resource Report Resource Website 1+ mentions |
Deep Blue Epigenomic Data Server (RRID:SCR_017490) | software resource, data access protocol, web service, service resource, data or information resource, access service 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 | 2026-02-15 09:22:07 | 2 |
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