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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SOAPfusion Resource Report Resource Website 1+ mentions |
SOAPfusion (RRID:SCR_000079) | SOAPfusion | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards. | software, open source, free, RNA, sequencing, data, computing, research, analysis, rna-seq, candidate regions, bio.tools |
is listed by: OMICtools is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Guangdong Innovative Research Team Program ; General Research Fund of the Hong Kong Government |
PMID:24123671 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01358, biotools:soapfusion | https://bio.tools/soapfusion | SCR_000079 | 2026-08-01 12:01:08 | 3 | |||||
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International Union of Basic and Clinical Pharmacology Resource Report Resource Website 1+ mentions |
International Union of Basic and Clinical Pharmacology (RRID:SCR_000135) | IUPHAR | nonprofit organization | Voluntary, non-governmental, non-profit pharmacologist association promoting international cooperation, sponsoring international and regional activities, encouraging free exchange of scientists and ideas, developing public awareness, establishing advisory committees. Has official relations with the World Health Organization (WHO). Helps pharmacologists to participate with other branches of science in international activities, either directly or under ICSU, WHO and UNESCO. Member of the International Council for Science (ICSU) and participates in the work of its scientific committees. Has its own publishing program. Pharmacology International, is published every June and December. Member Directory is maintained continually, as an online resource. Provides IUPHAR Receptor Database, major on-line repository of characterization data for receptors and drugs, and the IUPHAR Ion Channels Database. Official Reports from The IUPHAR Committee on Receptor Nomenclature and Drug Classification are published in Pharmacological Reviews. IUPHAR World Congresses of Pharmacology are held every few years. | gold standard, pharmacologist, association, international, receptor, nomenclature, drug, classification, data, repository |
is parent organization of: NC-IUPHAR is parent organization of: Endogenous GPCR List works with: CellPhoneDB |
Crossref funder ID: 100009703, nlx_47304, grid.479924.5 | https://ror.org/0125syc65 | SCR_000135 | International Union of Pharmacology | 2026-08-01 12:01:09 | 6 | |||||||
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Telethon Network of Genetic Biobanks Resource Report Resource Website 10+ mentions |
Telethon Network of Genetic Biobanks (RRID:SCR_004658) | TNGB | biomaterial supply resource, material resource | Network of non profit association of Italian repositories to form catalogue of biospecimens and associated data. Used to collect, process, preserve and distribute biological samples and related clinical data from individuals affected by rare diseases, their relatives or from healthy control individuals, with standards complying with Italian laws and international recommendations. You may browse sample catalogue by diagnosis or use advanced search option. Request for samples is granted only if project is in agreement with TNGB mission and after receiving signed material transfer agreement form. | Italian, repository, catalogue, biospeciment, data, collect, process, preserve, distribute, rare, disease |
is listed by: One Mind Biospecimen Bank Listing is affiliated with: EuroBioBank has parent organization: Telethon Foundation |
Telethon Foundation ; Italian Health Department |
PMID:24004821 | Restricted | nlx_65989 | SCR_004658 | Telethon Network of Genetic Biobanks | 2026-08-01 12:10:47 | 29 | |||||
|
Allen Brain Atlas Tools Resource Report Resource Website |
Allen Brain Atlas Tools (RRID:SCR_023855) | ABAT | software resource | Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas. | Allen Human Brain Atlas, MATLAB functions, Allen Brain Atlas data, data, read, analyze, visualize | is related to: Allen Institute for Brain Science | Free, Freely available | SCR_023855 | ABAT (Allen Brain Atlas Tools) | 2026-08-01 12:08:23 | 0 | ||||||||
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Cerner Enviza Resource Report Resource Website |
Cerner Enviza (RRID:SCR_024435) | commercial organization | American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases. | Oracle, Cerner, data, analytics, oncology, rare disease, | SCR_024435 | 2026-08-01 12:08:02 | 0 | ||||||||||||
|
elmr Resource Report Resource Website |
elmr (RRID:SCR_017249) | software toolkit, software resource | Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package. | support, working, light, electron, microscopy, fly, brain, data | is related to: NeuroAnatomy Toolbox | Free, Available for download, Freely available | https://jefferis.github.io/elmr/ | SCR_017249 | 2026-08-02 09:07:29 | 0 | |||||||||
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metagear Resource Report Resource Website |
metagear (RRID:SCR_017085) | software toolkit, software resource | Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis. | sythesis, taxonomy, systematic, review, assemble, screen, literature, extract, meta, data, analysis, statistical |
is listed by: CRAN is related to: R Project for Statistical Computing has parent organization: University of South Carolina; South Carolina; USA |
NSF DBI-1262545; NSF DEB-1451031 |
DOI:10.1111/2041-210X.12472 | Free, Available for download, Freely available | https://github.com/cran/metagear, https://lajeunesse.myweb.usf.edu | SCR_017085 | 2026-08-02 09:07:40 | 0 | |||||||
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clustLasso Resource Report Resource Website 1+ mentions |
clustLasso (RRID:SCR_018820) | software toolkit, software resource | Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach. | Predictive signatures, microbial phenotype, cluster lasso approach, build predictive signature, phenotype, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:clustlasso | https://bio.tools/clustlasso | SCR_018820 | 2026-08-02 09:07:53 | 1 | ||||||||
|
Cocoframer Resource Report Resource Website |
Cocoframer (RRID:SCR_023817) | software toolkit, software resource | Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer. | Allen Mouse Brain Atlas, Common Coordinate Framework, retrieving 3D, CCF aligned, gridded ISH, data, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023817 | COmmon COordinate FRAMEwork in R | 2026-08-02 09:09:05 | 0 | |||||||||
|
Sanford Burnham Prebys Medical Discovery Institute X-ray Crystallography Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute X-ray Crystallography Facility (RRID:SCR_014860) | material resource, instrument supplier | Facility equipped with X-ray crystallography equipment, such as the Rigaku FR-E SuperBright Ultra high-intensity rotating anode generator. The instrument is inteded for self-usage by trained users. It utilizes both ports with two independent diffraction stations that can run simultaneously. Each station is equipped with an X-stream cryogenic system for standard low temperature (~100 K) data collection. The system is used to collect high resolution diffraction data from native and inhibitor-bound crystals or to test and optimize diffraction quality (cryo-protectant conditions, etc.) and screen for further data collection at synchrotron sources. | x ray, crystallography, diffraction, data, inhibitor-bound crystals, synchrotron | Commercially available | SCR_014860 | SBP X-ray Crystallography Facility, SBP Medical Discovery Institute X-ray Crystallography Facility | 2026-08-03 09:35:55 | 0 | ||||||||||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-08-04 09:43:12 | 1 | |||||||||
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CropSight Resource Report Resource Website 1+ mentions |
CropSight (RRID:SCR_016870) | data access protocol, software resource, web service | Software tool which is a PHP and SQL based server platform. Provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management. | PHP, SQL, server, platform, automated, data, collation, storage, information, management, IoT sensor, phenotyping | Free, Available for download, Freely available, Registration required | SCR_016870 | 2026-08-04 09:44:00 | 1 | |||||||||||
|
Java Treeview Resource Report Resource Website 50+ mentions |
Java Treeview (RRID:SCR_016916) | TreeView | data processing software, data visualization software, software application, software resource | Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure. | gene, expression, data, visualization, microarray, interactive, display, cluster, dataset |
is related to: University of Hamburg; Hamburg; Germany has parent organization: Princeton University; New Jersey; USA |
Free, Available for download, Freely available | https://bitbucket.org/TreeView3Dev/treeview3/ | SCR_016916 | TreeView3, Treeview, Java TreeView | 2026-08-04 09:44:01 | 52 | |||||||
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Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | data processing software, data visualization software, software application, software resource | Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. | quantitative, visualization, aligned, RNA-Seq, read, data, compare, exon, usage, sample, experiment, condition, MISO | is related to: MISO | NCI R01 CA157304; Starr Cancer Consortium ; NIGMS R01 GM096193; NSF IIS 1149662; Alfred P. Sloan research fellowship ; NIGMS R01 GM085319; NCI U01 CA184897; NHGRI R01 HG002439 |
PMID:25617416 DOI:10.1093/bioinformatics/btv034 |
Free, Available for download, Freely available | http://miso.readthedocs.org/en/fastmiso/sashimi.html | SCR_016861 | sashimi_plot | 2026-08-04 09:44:00 | 0 | |||||
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tidyr Resource Report Resource Website 50+ mentions |
tidyr (RRID:SCR_017102) | software application, software resource, data management software | Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data. | tidy, data, spread, gather, function |
is used by: PlotsOfData is used by: tidyverse is listed by: CRAN is related to: R Project for Statistical Computing works with: dplyr |
Free, Available for download, Freely available | https://github.com/tidyverse/tidyr, https://tidyr.tidyverse.org/ | SCR_017102 | 2026-08-04 09:44:06 | 62 | |||||||||
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CDC Diseases & Conditions Resource Report Resource Website 1+ mentions |
CDC Diseases & Conditions (RRID:SCR_017070) | data or information resource, controlled vocabulary | List of diseases and conditions on Centers for Disease Control and Prevention website., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | vocabulary, list, data, condition, center, disease, control, prevention | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017070 | 2026-08-04 09:44:04 | 3 | |||||||||||
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vini: A viewer for fMRI data Resource Report Resource Website |
vini: A viewer for fMRI data (RRID:SCR_017250) | data processing software, data visualization software, software application, software resource | Software Python tool as viewer for MRI data and numpy arrays. | viewer, MRI, data, numpy, array | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | https://github.com/lipsia-fmri/vini | SCR_017250 | 2026-08-04 09:44:09 | 0 | |||||||||
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MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, software resource, web service | 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 | 2026-08-04 09:44:06 | 11 | ||||||
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Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-08-04 09:44:14 | 4 | ||||||
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BioWheel Resource Report Resource Website |
BioWheel (RRID:SCR_017441) | data processing software, data visualization software, software application, 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 | 2026-08-04 09:44:08 | 0 |
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