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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Fluorescent Imaging Analysis Software FIMAS Resource Report Resource Website 1+ mentions |
Fluorescent Imaging Analysis Software FIMAS (RRID:SCR_018311) | FIMAS | data processing software, image analysis software, software application, software resource | Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files. | Analysis procedure, fluorescent microscopy, fluorescent imaging, microscopy data, image processing, fluorescent data | uses: MATLAB | Free, Freely available | SCR_018311 | 2026-09-03 05:00:07 | 3 | |||||||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | data processing software, software application, software resource | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; JSPS KAKENHI ; Wellcome Trust |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-09-03 05:00:20 | 2 | |||||
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Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System Resource Report Resource Website 10+ mentions |
Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System (RRID:SCR_018436) | instrument resource | Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C. | Matrix Assisted Laser Desorption Ionization Time of Flight Instrument, Instrument, Equipment, Applied Biosystems, USEDit, ABRF | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018436.pdf | SCR_018448, SCR_019577, Model_Number_9700 | https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_040970.pdf | SCR_018436 | 2026-09-03 05:00:23 | 13 | ||||||||
|
Certified Genetool, Inc. Resource Report Resource Website |
Certified Genetool, Inc. (RRID:SCR_018678) | data or information resource, organization portal, portal, service resource | Provides services for USED lab instrument repairs.Recertified laboratory equipment commercially available. Comes fully re-certified to manufacturers standards with 90 day warranty. | USEDit, used lab instrument service, repair service, recertified laboratory equipment, manufacturer standard, ABRF, ABRF | is listed by: ABRF CoreMarketplace | Restricted | ABRF_835 | https://coremarketplace.org/?FacilityID=835 | SCR_018678 | Inc., Certified Genetool | 2026-09-03 05:00:08 | 0 | |||||||
|
Dimensions COVID-19 publications, datasets and clinical trials Resource Report Resource Website |
Dimensions COVID-19 publications, datasets and clinical trials (RRID:SCR_018276) | data or information resource, portal | All Dimensions publications, datasets, and clinical trials related to COVID-19, updated daily. | COVID-19, COVID-19 data, COVID-19 literature, COVID-19 clinical trials | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018276 | 2026-09-03 05:00:22 | 0 | |||||||||
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CoMSES Net Resource Report Resource Website 1+ mentions |
CoMSES Net (RRID:SCR_017598) | data or information resource, organization portal, portal | Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse. | Develop, share, reuse, computational, model, social, ecological, system, network, repository, citation, digital, preservation, reproducibility, archive | is listed by: DataCite | Restricted | DOI:10.25937 | https://doi.org/10.25937/, https://dx.doi.org/10.25937/ | SCR_017598 | Network for Computational Modeling in Social and Ecological Sciences | 2026-09-03 05:00:05 | 6 | |||||||
|
Chinese National Compound Library Resource Report Resource Website 1+ mentions |
Chinese National Compound Library (RRID:SCR_018723) | CNCL | data or information resource, organization portal, portal | Library with storage capacity of over million compounds possessing diversified structures. Coupled with this library will be advanced sample handling, information management and quality control systems. As important material and information resource, CNCL will work with both domestic and international stakeholders to promote sustained development of Chinese pharmaceutical industry. | Library, compound library, compound, diversified structure, sample handling, information management, quality control, pharmaceutical industry | SCR_018723 | 2026-09-03 05:01:06 | 1 | |||||||||||
|
refine.bio Resource Report Resource Website 1+ mentions |
refine.bio (RRID:SCR_017471) | data processing software, software application, software resource | Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists. | Process, normalize, large, amount, data, cancer, dataset, standardized, pipeline, gene, expression | Free, Available for download, Freely available | https://www.refine.bio/ | SCR_017471 | 2026-09-03 04:59:57 | 1 | ||||||||||
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JTK_CYCLE Resource Report Resource Website 1+ mentions |
JTK_CYCLE (RRID:SCR_017962) | data processing software, software application, software resource | Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets. | Washington University in St.Louis, detecting rhythmic, component, genome, scale, dataset, algorithm, non parametric, cycling, variable | NHBLI R01 HL097800; NIMH P50 MH074924; Pennsylvania Commonwealth Health Research Formula Funds |
PMID:20876817 | Free, Freely available | SCR_017962 | Jonckheere-Terpstra-Kendall-CYCLE | 2026-09-03 04:59:58 | 5 | ||||||||
|
Cancer Imaging Phenomics Toolkit Resource Report Resource Website 10+ mentions |
Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) | CaPTk | data processing software, image analysis software, software application, software resource | Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome. | analysis, radiographic, cancer, image, quantitative, analytics | is related to: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | Cancer | NCI U24 CA189523 | PMID:29340286 | Free, Available for download, Freely available | https://github.com/CBICA/CaPTk/ | SCR_017323 | Cancer Imaging Phenomics Toolkit | 2026-09-03 05:01:01 | 11 | ||||
|
QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | data processing software, image analysis software, software application, software resource | Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images. | Digital pathology, image analysis, whole slide image, batch processing, tissue image, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Queens University Belfast; Ireland; United Kingdom |
Cancer Research UK Accelerator ; Experimental Cancer Medicine Centre Network ; Friends of the Cancer Centre ; Invest Northern Ireland ; Sean Crummey Memorial Fund ; Tom Simms Memorial Fund |
PMID:29203879 | Free, Available for download, Freely available | biotools:qupath | https://bio.tools/qupath | SCR_018257 | 2026-09-03 05:00:22 | 2084 | ||||||
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Neural Ideal Resource Report Resource Website |
Neural Ideal (RRID:SCR_017448) | data processing software, software application, software resource | Software package for extracting neural activity codes. | Extracting, neural, activity, code, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB |
NIBIB EB022862 | Free, Available for download, Freely available | SCR_017448 | 2026-09-03 05:00:31 | 0 | |||||||||
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MountainSort Resource Report Resource Website 10+ mentions |
MountainSort (RRID:SCR_017446) | data processing software, software application, software resource | Neurophysiological spike sorting software. | Neurophysiological, spike, sorting, BRAIN Initiative | is recommended by: BRAIN Initiative | NINDS NS090537 | Free, Available for download, Freely available | SCR_017446 | 2026-09-03 05:00:04 | 15 | |||||||||
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Wikidata Resource Report Resource Website 10+ mentions |
Wikidata (RRID:SCR_018492) | data or information resource, portal, project portal | Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects. | Open knowledge base, structured data storage, Wikimedia data, Wikipedia data, Wikivoyage data, Wiktionary data, Wikisource data |
lists: Scholia is related to: Author Disambiguator is related to: Clinical Trials Wiki Loader is related to: ClinWiki is related to: VanderBot is related to: Mix n Match is related to: Scholia is related to: QuickStatements is related to: Wikidata Query Service is related to: Author Disambiguator is related to: TABernacle is related to: OpenRefine is related to: SourceMD |
Free, Freely available | Wikidata_Q2013 | https://www.wikidata.org/wiki/Q2013 | SCR_018492 | 2026-09-03 05:01:05 | 47 | ||||||||
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hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | data processing software, software application, software resource, software toolkit | Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis. | Quantitative, MRI, data, processing, multi, parameter, qMRI, map, spatial, registration, statistical, analysis, histology, longitudinal, relaxation, rate R1 and R2, proton, density, magnetisation, transfer, MT saturation |
is related to: MATLAB is related to: SPM |
Belgian Walloon Government ; Emory Universitys Research Council ; European Regional Development Fund ; European Research Council ; European Structural and Investment Fund ; German Research Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Swedish Research Council ; Swiss National Science Foundation ; Swiss State Secretariat for Education ; Research and Innovation ; Wellcome Trust |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-09-03 05:01:03 | 37 | |||||||
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Scmap Resource Report Resource Website 10+ mentions |
Scmap (RRID:SCR_017338) | data processing software, software application, software resource | Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments. | Unsupervised, projection, single, cell, RNA-seq, data |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:29608555 | Free, Available for download, Freely available | http://bioconductor.org/packages/scmap/, https://www.sanger.ac.uk/science/tools/scmap | SCR_017338 | 2026-09-03 05:00:18 | 17 | ||||||||
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GeSeq Resource Report Resource Website 500+ mentions |
GeSeq (RRID:SCR_017336) | data processing software, service resource, software application, software resource | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
German Science Foundation ; Human Frontier Science Program ; Max Planck Society |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-09-03 04:59:56 | 535 | ||||||
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FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | data processing software, software application, software resource | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NDSEG Fellowship ; NIAID R21 AI115014; NSF Graduate Research Fellowship DGE 0940902; NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; Welch Foundation |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-09-03 05:00:21 | 6 | |||||
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Neuron Tools Resource Report Resource Website 1+ mentions |
Neuron Tools (RRID:SCR_017450) | data processing software, software application, software resource | Software tools for converting data files into persistence diagrams and distance matrices. | Converting, data, file, diagram, distance, matice, BRAIN Initiative | is recommended by: BRAIN Initiative | NIBIB EB022899 | Free, Available for download, Freely available | SCR_017450 | 2026-09-03 05:01:01 | 3 | |||||||||
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Stereo Investigator - Cleared Tissue Edition Resource Report Resource Website |
Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) | data processing software, image analysis software, software application, software resource | Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses. | Stereology, cleared, tissue, intact, speciment, imaged, confocal, microscopy, analysis, MBF Bioscience | Restricted | SCR_017668 | 2026-09-03 05:00:20 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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