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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cerebrovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) | CDKP | data or information resource, database, disease-related portal, portal, topical portal | Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data. | human, genetic, information, cerebrovascular, disease, data, knowledge |
is listed by: NIDDK Information Network (dkNET) has parent organization: Massachusetts General Hospital Labs and Facilities |
cerebrovascular disease | Accelerating Medicines Partnership in Type 2 Diabetes ; NIH ; NINDS |
Free, Available for download | SCR_016535 | SCR_015628 | Cerebrovascular Disease Knowledge Portal (CDKP) | 2026-08-29 11:24:59 | 17 | |||||
|
BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | data processing software, data visualization software, software application, software resource, web application | Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. | Box plot generation, customized box plot, data, plot, analysis |
is listed by: SoftCite is related to: PlotsOfData is related to: vioplot |
ERC ; Genome Québec International Recruitment Award ; Wellcome Trust ; WTCCB |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | 2026-08-29 11:25:02 | 370 | ||||||
|
primers4clades Resource Report Resource Website 1+ mentions |
primers4clades (RRID:SCR_015714) | software resource, web application | Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs. | pcr primer, metagenomic dna, phylogenetic lineage, primer, clade, bio.tools |
is listed by: Debian is listed by: bio.tools |
DGAPA IN201806-2; CONACyT-Mexico P1-60071; CSIC 200720I038 |
PMID:19465390 | Freely available, Free for academic use, Tutorial available | biotools:primers4clades | http://maya.ccg.unam.mx/primers4clades, https://bio.tools/primers4clades | SCR_015714 | 2026-08-29 11:25:03 | 2 | ||||||
|
ARCHS4 Resource Report Resource Website 50+ mentions |
ARCHS4 (RRID:SCR_015683) | software tool | ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome. | SCR_015683 | 2026-08-29 11:25:03 | 84 | |||||||||||||
|
Cuffmerge Resource Report Resource Website 500+ mentions |
Cuffmerge (RRID:SCR_015688) | software tool | The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53. | SCR_015688 | 2026-08-29 11:25:18 | 951 | |||||||||||||
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clustergrammer Resource Report Resource Website 10+ mentions |
clustergrammer (RRID:SCR_015681) | data visualization tool, software tool | Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features. | bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/sdata.2017.151 | biotools:clustergrammer | https://bio.tools/clustergrammer | SCR_015681 | 2026-08-29 11:25:17 | 48 | ||||||||
|
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 | 2026-08-29 11:25:04 | 1 | ||||||||||
|
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 | 2026-08-29 11:25:00 | 1808 | |||||
|
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 | 2026-08-29 11:25:19 | 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 | 2026-08-29 11:25:01 | 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 | 2026-08-29 11:25:03 | 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 | 2026-08-29 11:25:03 | 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 | 2026-08-29 11:25:00 | 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 | 2026-08-29 11:25:00 | 5 | |||||||
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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 | 2026-08-29 11:25:19 | 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 | 2026-08-29 11:25:03 | 1 | |||||||||||||
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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 | 2026-08-29 11:25:17 | 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’ | 2026-08-29 11:25:17 | 13 | |||||||||
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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 | 2026-08-29 11:25:02 | 1577 | |||||||||
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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 | 2026-08-29 11:24:59 | 2 |
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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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