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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BPG Resource Report Resource Website 1+ mentions |
BPG (RRID:SCR_023652) | software toolkit, software resource | Software R package contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in creation of these plots. Functions to create publication quality plots. | Create publication quality plots, plotting functions, barplots, scatterplots, heatmaps, | Government of Ontario ; Movember Foundation ; Terry Fox Research Institute New Investigator Award ; Canadian Institutes of Health Research New Investigator Award ; Canadian Cancer Society ; Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Foundation for Innovation ; Canadian Breast Cancer Foundation ; Ontario Genomics Institute ; Medical Biophysics Excellence University of Toronto Fund Scholarship ; EU 7th framework program |
PMID:30665349 | Free, Available for download, Freely available | https://github.com/uclahs-cds/public-R-BoutrosLab-plotting-general | SCR_023652 | BoutrosLab.plotting.general | 2026-08-02 09:09:01 | 1 | |||||||
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brms Resource Report Resource Website 1+ mentions |
brms (RRID:SCR_023862) | software toolkit, software resource | Software package implements Bayesian multilevel models in R using probabilistic programming language Stan. | Bayesian multilevel models, R, probabilistic programming language Stan, | is listed by: CRAN | DOI:10.18637/jss.v080.i01 | Free, Available for download, Freely available | SCR_023862 | 2026-08-02 09:08:55 | 2 | |||||||||
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vtree Resource Report Resource Website 1+ mentions |
vtree (RRID:SCR_023458) | software toolkit, software resource | Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame. | Display information, nested subsets, data frame, calculating and drawing variable trees, variable trees | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/nbarrowman/vtree | SCR_023458 | variable tree | 2026-08-02 09:08:58 | 1 | ||||||||
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DeepSlice Resource Report Resource Website 1+ mentions |
DeepSlice (RRID:SCR_023854) | software toolkit, software resource | Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning. | Allen Mouse Brain Atlas, Common Coordinate Framework, Allen Brain Atlas, Waxholm rat atlas, aligns histology, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023854 | 2026-08-02 09:08:55 | 3 | ||||||||||
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Cell Type Analysis Toolbox Resource Report Resource Website |
Cell Type Analysis Toolbox (RRID:SCR_023852) | software toolkit, software resource | Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data. | Allen Mouse Brain Atlas, cell counting and distribution mapping, serial two-photon tomography data, STPT data, data analysis, | is related to: Allen Institute for Brain Science | PMID:28985566 | Free, Freely available | SCR_023852 | 2026-08-02 09:09:06 | 0 | |||||||||
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Reads2Map Resource Report Resource Website 1+ mentions |
Reads2Map (RRID:SCR_023593) | software toolkit, software resource | Software package as collection of WDL workflows to build linkage maps from sequencing reads. WDL workflows to build genetic maps from sequencing reads. | Genetic Map, Linkage analysis, Variant Calling, Dosage Calling | National Council for Scientific and Technological Development 313269/2021-1; USDA National Institute of Food and Agriculture (NIFA); 2020-51181-32156 Bill and Melinda Gates Foundation; OPP1213329 European Union’s Horizon 2020 |
DOI:10.1101/2022.11.24.517847 | Free, Available for download, Freely available | SCR_023593 | 2026-08-02 09:09:00 | 1 | |||||||||
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DESDEO Resource Report Resource Website 1+ mentions |
DESDEO (RRID:SCR_023502) | software toolkit, software resource | Software Python framework for interactive multiobjective optimization methods. | interactive multiobjective optimization, optimization methods, | DOI:10.1109/ACCESS.2021.3123825 | Free, Available for download, Freely available | https://desdeo.it.jyu.fi/, https://desdeo.readthedocs.io/en/latest/ | SCR_023502 | Decision Support for computationally Demanding Optimization | 2026-08-02 09:08:38 | 1 | ||||||||
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clusterSim Resource Report Resource Website 10+ mentions |
clusterSim (RRID:SCR_023743) | software toolkit, software resource | Software R package used for searching for optimal clustering procedure for data set. | searching for optimal clustering procedure for data set, optimal clustering procedure, data set clustering procedure, | is listed by: CRAN | Free, Freely available | SCR_023743 | 2026-08-02 09:08:52 | 20 | ||||||||||
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Frictionless Data Resource Report Resource Website 1+ mentions |
Frictionless Data (RRID:SCR_023713) | software toolkit, software resource | Open source software package for building data infrastructure including data management, data integration, data flows, etc. Includes various data standards and provides software to work with data. | building data infrastructure, data management, data integration, data flows, data standards information, | Free, Available for download, Freely available | https://github.com/frictionlessdata | SCR_023713 | 2026-08-02 09:08:39 | 3 | ||||||||||
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Rprs Resource Report Resource Website 1+ mentions |
Rprs (RRID:SCR_023557) | Rprs | software toolkit, software resource | Software R package for computing Polygenic Risk Scores from dosages. | computing Polygenic Risk Scores from Polygenic Risk Scores, Polygenic Risk Scores, Polygenic Risk Scores | Free, Available for download, Freely available | SCR_023557 | Polygenic Risk Scores | 2026-08-02 09:08:48 | 1 | |||||||||
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easyPubMed Resource Report Resource Website 1+ mentions |
easyPubMed (RRID:SCR_023570) | software toolkit, software resource | Software R package for query NCBI Entrez and retrieve PubMed records in XML or text format. Used to process PubMed records by extracting and aggregating data from selected fields. Large number of records can be downloaded via this simple-to-use interface to NCBI PubMed API. Used to search and retrieve scientific publication records from PubMed. | Search and retrieve scientific publication records, scientific publication records, PubMed | Free, Available for download, Freely available | https://www.data-pulse.com/dev_site/easypubmed/ | SCR_023570 | 2026-08-02 09:09:00 | 3 | ||||||||||
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Preprocessing tools for oligonucleotide arrays Resource Report Resource Website 10+ mentions |
Preprocessing tools for oligonucleotide arrays (RRID:SCR_023726) | software toolkit, software resource | Software R package to analyze oligonucleotide arrays at probe level. Supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). Used for annotation of Affymetrix Gene Array data. | analyze oligonucleotide arrays, Affymetrix Gene Array, NimbleGen array, Affymetrix Gene Array data annotation, | Brazilian Funding Agency CAPES ; NCRR R01 RR021967; NHGRI P41 HG004059 |
PMID:20688976 | Free, Available for download, Freely available | SCR_023726 | affycoretools | 2026-08-02 09:08:52 | 13 | ||||||||
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ARA Tools Resource Report Resource Website 1+ mentions |
ARA Tools (RRID:SCR_023826) | software toolkit, software resource | Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. Collection of MATLAB functions to analyze mouse whole brain imaging data and the associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas. | Allen Mouse Brain Reference Atlas, analyze mouse whole brain imaging data, cell locations, traced neurite trees, traced projections from bulk injection, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023826 | 2026-08-02 09:09:05 | 1 | ||||||||||
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VirusDetect Resource Report Resource Website 10+ mentions |
VirusDetect (RRID:SCR_023669) | software toolkit, software resource | Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs. | Virus discovery, analyze large scale sRNA datasets, virus identification, deep sequencing of small RNAs, sequencing, small RNAs | NSF | PMID:27825033 | Free, Available for download, Freely available | https://github.com/kentnf/VirusDetect | SCR_023669 | 2026-08-02 09:09:02 | 16 | ||||||||
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Process Genes List Resource Report Resource Website |
Process Genes List (RRID:SCR_023823) | PGL | software toolkit, software resource | Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results. | Allen Human Brain Atlas | is related to: Allen Institute for Brain Science | PMID:32201351 | Free, Available for download, Freely available | SCR_023823 | 2026-08-02 09:08:54 | 0 | ||||||||
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PET-CT mouse brain toolbox Resource Report Resource Website |
PET-CT mouse brain toolbox (RRID:SCR_023821) | software toolkit, software resource | Software toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images. | Allen Mouse Brain Atlas, murine image template, mouse PET-CT brain images, | is related to: Allen Institute for Brain Science | DOI:10.1038/s41598-022-19872-4 | Free, Freely available | SCR_023821 | 2026-08-02 09:08:54 | 0 | |||||||||
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BLIMP: Biomedical LIterature Mining Publications Resource Report Resource Website 1+ mentions |
BLIMP: Biomedical LIterature Mining Publications (RRID:SCR_007112) | BLIMP | data or information resource, bibliography | Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication. | biomedical, literature, text mining, bibliography, journal, text, biomedicine, natural language processing, information extraction, information retrieval, text categorization, ontology | has parent organization: Queens University; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada ; Queen's University Principal's Development Award ; NSERC Discovery 298292-04 |
The community can contribute to this resource | nif-0000-21063 | SCR_007112 | Biomedical LIterature (and text) Mining Publications | 2026-08-03 09:33:22 | 1 | ||||||
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Bio-Rad: ZE5 Cell Analyzer Resource Report Resource Website 1+ mentions |
Bio-Rad: ZE5 Cell Analyzer (RRID:SCR_019712) | instrument resource | BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals. | Bio Rad, Cytometer, Instrument, Equipment, Usedit | Commercially available | SCR_019713, Model_Number_ZE5, SCR_019717 | SCR_019712 | , Bio-Rad ZE5 Cell Analyzer Flow Cytometer, BioRad ZE5, Bio-Rad ZE5/Yeti Cell Analyzer Flow Cytometer | 2026-08-03 09:37:13 | 6 | |||||||||
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GE: Biacore 3000 Real Time Biomolecular Interaction Analyzer Resource Report Resource Website 1+ mentions |
GE: Biacore 3000 Real Time Biomolecular Interaction Analyzer (RRID:SCR_018044) | instrument resource | Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants. | ABRF, Real Time Biomolecular Interaction Analyzer, GE Healthcare, instrument, equipment | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018044.pdf | SCR_019676, SCR_018577, Model_Number_Biacore 3000 | https://www.ibps.sorbonne-universite.fr/ressources/documents/1/2276, Brochure-Biacore-3000.pdf | https://www.gelifesciences.com/en/us/shop/biacore-3000-goldseal-p-02795 | SCR_018044 | BIACORE 3000 GOLDSEAL, BiaCore 3000 Surface Plasmon Resonance | 2026-08-03 09:37:11 | 4 | |||||
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University of Oklahoma; Oklahoma; USA Resource Report Resource Website 1+ mentions |
University of Oklahoma; Oklahoma; USA (RRID:SCR_001074) | OU | university | A coeducational public research university located in Oklahoma, USA. The institution confers undergraduate and graduate degrees in fields such as law, medicine, aviation, energy management, history of science, and Native American studies. | public, research, university, undergraduate, graduate |
is parent organization of: Development of a Specific-Pathogen-Free Baboon Colony is parent organization of: University of Oklahoma College of Medicine; Oklahoma; USA is parent organization of: Amblyomma Americanum (Lone Star Tick) cDNA Sequencing is parent organization of: Baboon Research Resouces is parent organization of: Cryptococcus Neoformans cDNA Sequencing is parent organization of: University of Oklahoma Labs and Facilities is parent organization of: University of Oklahoma Health Sciences Center Laboratory for Molecular Biology and Cytometry Research Core Facility is parent organization of: University of Oklahoma Samuel Roberts Nobel Microscopy Laboratory Core Facility is parent organization of: University of Oklahoma Health Sciences Center OK INBRE Data Science Core Facility is parent organization of: University of Oklahoma Protein Production and Characterization Core Facility is parent organization of: University of Oklahoma Biomolecular Structure Core Facility is parent organization of: University of Oklahoma Health Sciences Center Tissue Pathology and Biospecimen Core Facility is parent organization of: University of Oklahoma College of Medicine Immunology and Informatics Core Facility |
nlx_27458, grid.266900.b, Wikidata:Q640652, ISNI:0000 0004 0447 0018, Crossref funder ID:100007926 | https://ror.org/02aqsxs83 | SCR_001074 | University of Oklahoma | 2026-08-03 09:31:13 | 1 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
