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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Dynamic Spatial Illuminator Software Resource Report Resource Website 1+ mentions |
Dynamic Spatial Illuminator Software (RRID:SCR_015725) | software resource | Software used in tandem with the Polygon 400 from Mightex systems to define areas of illumination, control light intensity and duration, and calibrate the device. | illumination, light intensity, device calibration, mightex system, polygon 400, spatial resolution | Commercially available, Available for purchase | http://www.mightexsystems.com/family_info.php?cPath=245_347_346&categories_id=346 | SCR_015725 | 2026-09-19 12:53:11 | 1 | ||||||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | data analysis software, data processing software, software application, software resource, source code | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-09-19 12:53:11 | 1808 | |||||
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BSVF Resource Report Resource Website 1+ mentions |
BSVF (RRID:SCR_015727) | BSVF | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries. | virus integration, sequencing analysis, virus assembly, integration, bisulfite, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:bs-virus-finder | https://bio.tools/bs-virus-finder | SCR_015727 | BSVF: Bisulfite Sequencing Virus integration Finder, Bisulfite Sequencing Virus integration Finder | 2026-09-19 12:53:11 | 1 | ||||||
|
Glo-Max Multi Detection System Resource Report Resource Website 1+ mentions |
Glo-Max Multi Detection System (RRID:SCR_015575) | resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 6, 2017. Detection instrument that gathers absorbance, fluorescence, and luminescence data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | detection instrument, absorbance machine, fluorescence machine, luminescence machine, hardware, instrument, equipment | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015575 | Glo Max Multi Detection System, GloMax Multi Detection System | 2026-09-19 12:53:09 | 9 | ||||||||||
|
Torrent Variant Caller Standalone Resource Report Resource Website 10+ mentions |
Torrent Variant Caller Standalone (RRID:SCR_015694) | software tool | A variant vcf file analysis tool. | http://updates.iontorrent.com/tvc_standalone/ | SCR_015694 | 2026-09-19 12:53:11 | 41 | ||||||||||||
|
GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | electronic laboratory notebook, software application, software resource, systems interoperability software, web application | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | GenePattern Notebook environment | 2026-09-19 12:53:11 | 3 | |||||
|
University of Pennsylvania Diabetes Research Center Resource Report Resource Website 1+ mentions |
University of Pennsylvania Diabetes Research Center (RRID:SCR_015732) | DRC | data or information resource, disease-related portal, portal, topical portal | NIDDK center that serves diabetes-oriented investigators from University of Pennsylvania as well as additional institutions from the mid-Atlantic region. The Penn DRC represents many basic science and clinical departments at Penn and the other institutions, and supports research in diabetes and obesity via Scientific Cores, a Pilot and Feasibility Grant Program, and a series of seminars, retreats, and other academic enrichment activities. | diabetes, research, univeristy of pennsylvania, upenn, obesity, metabolic disorder | is listed by: NIDDK Information Network (dkNET) | NIDDK P30DK19525 | Available to affiliated researchers | http://www.med.upenn.edu/, https://diabetescenters.org/ | SCR_015732 | 2026-09-19 12:53:11 | 1 | |||||||
|
IITC Life Sciences: Rotarod Test Resource Report Resource Website 1+ mentions |
IITC Life Sciences: Rotarod Test (RRID:SCR_015698) | instrument resource | Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard. | motor function, endurance, mouse, rat, drug resistance, material resource, hardware, instrument, equipment, USEDit |
is listed by: USEDit is related to: ANY-maze |
Commercially available | https://drive.google.com/file/d/18ukwQxS-8nMcPfZRWuBiBW8w-r429oR3/view?usp=drivesdk | https://www.iitcinc.com/pdf/Rotarod.pdf | SCR_015698 | IITC Rotarod Test, IITC Rotarod Treadmill, Rotarod Treadmill for mice and rats, IITC's Rotarod Test, Rotarod Test Rats and Mice, IITC Life Sciences Rotarod Treadmill | 2026-09-19 12:53:11 | 5 | |||||||
|
Functional Network Connectivity (FNC) Resource Report Resource Website 10+ mentions |
Functional Network Connectivity (FNC) (RRID:SCR_015731) | FNC | data analysis software, data processing software, software application, software resource, software toolkit | Software toolbox which finds and displays temporal relations amongst components. This can help determine causal relations in the brain. | fmri, temporal relation, causal relation, neural connectivity, | is used by: MATLAB | PMID:18082428 | Free, Available for download, Tutorial available | http://mialab.mrn.org/software/fnc/index.html | SCR_015731 | FNC Toolbox, GIFT toolbox, Functional Network Connectivity Toolbox | 2026-09-19 12:53:11 | 26 | ||||||
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Oncotopix Discovery Resource Report Resource Website 1+ mentions |
Oncotopix Discovery (RRID:SCR_015690) | software resource | Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background. | SCR_015690 | 2026-09-19 12:53:11 | 1 | |||||||||||||
|
R package: LMERConvenienceFunctions Resource Report Resource Website 1+ mentions |
R package: LMERConvenienceFunctions (RRID:SCR_015658) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software package that performs backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. | r, fixed effect, random effect, anova, p-value, r-squared, data trimming, data visualization | is listed by: CRAN | Free, Available for download | SCR_015658 | LMERConvenienceFunctions, Package ‘LMERConvenienceFunctions’, LMERConvenienceFunctions: Model Selection and Post-hoc Analysis for (G)LMER Models | 2026-09-19 12:53:10 | 5 | |||||||||
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R package: lattice Resource Report Resource Website 10+ mentions |
R package: lattice (RRID:SCR_015662) | data processing software, data visualization software, software application, software resource | Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements. | r, r package, multivariate data, data visualization | is listed by: CRAN | Free, Available for download | SCR_015662 | lattice, lattice: Trellis Graphics for R, Package ‘lattice’ | 2026-09-19 12:53:10 | 13 | |||||||||
|
GeneMarker Resource Report Resource Website 1000+ mentions |
GeneMarker (RRID:SCR_015661) | data analysis software, data processing software, software application, software resource | Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software. | genotype, gene analysis | is listed by: SoftCite | Commercially available, Trial available, Runs on Mac OS, Runs on Windows, Runs on Linux | SCR_015661 | GeneMarker: The Biologist Friendly Software | 2026-09-19 12:53:10 | 1577 | |||||||||
|
LabeledIn Resource Report Resource Website 1+ mentions |
LabeledIn (RRID:SCR_015667) | data or information resource, database, software resource | Database of annotations of drug indications in FDA drug labels. LabeledIn contains an expert curated set of indications and a crowdsourced set of indications. | drug, annotation, fda, fda drug label | Intramural Research Program of the NIH – National Library of Medicine ; National Key Technology R&D Program of China 2013BAI06B01; Fundamental Research Funds for the Central Universities 13R0101; MITRE Internal Research and Development Program |
PMID:25220766 PMID:25797061 |
Public, Freely available, Free, Available for download | SCR_015667 | 2026-09-19 12:53:10 | 2 | |||||||||
|
DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | data or information resource, database | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | 2026-09-19 12:53:10 | 655 | |||||||
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TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | data or information resource, database, software resource, web application | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-09-19 12:53:10 | 45 | |||||
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MIDAS Resource Report Resource Website 1+ mentions |
MIDAS (RRID:SCR_015704) | data processing software, image analysis software, image processing software, software application, software resource | Software for processing, display, and analysis of magnetic resonance spectroscopic imaging data. MIDAS supports a "whole-brain" MRSI acquisition method that has been implemented on MRI systems from three major manufacturers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mrsi, magnetic resonance spectroscopic imaging, processing software, brain imaging | NIBIB R01EB00822; NIBIB R01EB016064 |
PMID:16763967 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015704 | MIDAS Software, Metabolite Imaging and Data Analysis System, MIDAS: Metabolite Imaging and Data Analysis System | 2026-09-19 12:53:11 | 1 | ||||||||
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Evolutionary Rate Covariation Resource Report Resource Website 1+ mentions |
Evolutionary Rate Covariation (RRID:SCR_015669) | ERC | data analysis software, data processing software, software application, software resource, web application | Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes. | statistical software, correlation, phylogeny, gene extraction, genetic evolutionary history, covariation, group analysis | PMID:25679399 PMID:24453993 PMID:22287101 |
Freely available, Free, Available for download | SCR_015669 | ERC: Evolutionary Rate Covariation, Evolutionary Rate Covariation (ERC) Analysis, Evolutionary Rate Covariation (ERC) | 2026-09-19 12:53:10 | 2 | ||||||||
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Connectivity Map 02 Resource Report Resource Website 100+ mentions |
Connectivity Map 02 (RRID:SCR_015674) | cmap | data or information resource, database, software resource, web application | Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription, expression, gene, drug, disease pattern-matching algorithm, FASEB list |
has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
PMID:17008526 | THIS RESOURCE IS NO LONGER IN SERVICE | https://www.broadinstitute.org/cmap_build01 | SCR_015674 | Broad Institute Connectivity Map 02 Build, cmap | 2026-09-19 12:53:10 | 243 | ||||||
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Mendeley Data Resource Report Resource Website 100+ mentions |
Mendeley Data (RRID:SCR_015671) | data or information resource, data repository, service resource, storage service resource | Cloud-based data repository for storing, publishing and accessing scientific data. Mendeley Data creates a permanent location and issues Force 11 compliant citations for uploaded data. | data repository, published data, citation, force 11, doi, dans, dans (data archiving and networking services) |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: Mendeley works with: DANS |
Free, Public, The research community can contribute to this resource, Account required | DOI:10.25504/FAIRsharing.3epmpp, DOI:10.17616/R3DD11, r3d100011868, DOI:10.17632 | https://doi.org/10.17616/R3DD11, https://doi.org/10.17616/r3dd11, https://doi.org/10.17632/, https://dx.doi.org/10.17632/, https://fairsharing.org/10.25504/FAIRsharing.3epmpp, https://doi.org/10.17616/R3DD11 | SCR_015671 | 2026-09-19 12:53:10 | 239 |
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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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