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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ggplot2 Resource Report Resource Website 10000+ mentions |
ggplot2 (RRID:SCR_014601) | data processing software, data visualization software, software application, software resource | Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers. | plotting system, r, graphics, data analysis, multi-layered graphics, bio.tools |
uses: ggpubr uses: ggeffects uses: ggsignif is used by: riboWaltz is used by: ClustVis is used by: ggrepel is used by: PlotsOfData is used by: EnhancedVolcano is used by: tidyverse is used by: ComplexUpset is used by: ggfortify is used by: forestmodel is used by: ggvenn is used by: metaviz is used by: ggVennDiagram is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: ggraph is related to: ggbiplot is related to: GGally is related to: ggstatsplot is related to: ggpointdensity has parent organization: CRAN works with: Plotly works with: cowplot works with: ggalluvial works with: ggforce works with: ggbreak works with: ggrastr works with: tidybayes works with: ggsurvfit works with: ggtext works with: ggsci |
Free, Freely available | biotools:ggplot2 | http://docs.ggplot2.org/current/, https://github.com/tidyverse/ggplot2, https://bio.tools/ggplot2 | http://ggplot2.org/ | SCR_014601 | grammar of graphics plot2 | 2026-09-05 06:27:48 | 42192 | ||||||
|
ComplexUpset Resource Report Resource Website 10+ mentions |
ComplexUpset (RRID:SCR_022752) | data analysis software, data processing software, software application, software resource | Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries. | visualization of intersecting sets, set intSections in matrix layout, aggregates based on groupings and queries, quantitative analysis of sets |
uses: ggplot2 is listed by: CRAN |
Air Force Research Laboratory and DARPA ; Austrian Science Fund ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_022752 | 2026-09-05 06:30:16 | 25 | ||||||||
|
ggsignif Resource Report Resource Website 10+ mentions |
ggsignif (RRID:SCR_023047) | data analysis software, data processing software, software application, software resource | Software package to indicate if two groups are significantly different. Used to add significance brackets to ggplots. | indicate if two groups are significantly different, add significance brackets |
is used by: ggplot2 is listed by: CRAN |
Free, Available for download, Freely available | https://github.com/const-ae/ggsignif | SCR_023047 | 2026-09-05 06:30:18 | 21 | |||||||||
|
ggeffects Resource Report Resource Website 1+ mentions |
ggeffects (RRID:SCR_022496) | software resource, software toolkit | Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames. | Create tidy data frames of marginal effects, compute marginal effects, adjusted predictions, statistical models, tidy data frame |
is used by: ggplot2 is related to: CRAN |
Free, Available for download, Freely available | SCR_022496 | 2026-09-05 06:33:10 | 5 | ||||||||||
|
ggforce Resource Report Resource Website 1+ mentions |
ggforce (RRID:SCR_022575) | software resource, software toolkit | Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0. | missing functionality, ggplot2, extension system |
is related to: CRAN works with: ggplot2 |
Free, Available for download, Freely available | https://github.com/thomasp85/ggforce/, https://ggforce.data-imaginist.com/ | SCR_022575 | 2026-09-05 06:33:11 | 7 | |||||||||
|
cowplot Resource Report Resource Website 50+ mentions |
cowplot (RRID:SCR_018081) | data processing software, data visualization software, software application, software resource | Software R package as streamlined plot theme and plot annotations for ggplot2. Provides various features that help with creating publication quality figures with ggplot2, such as set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. | Plot, annotation, publication figure, image |
is listed by: CRAN works with: ggplot2 |
Free, Available for download, Freely available | https://wilkelab.org/cowplot/ | SCR_018081 | R package cowplot | 2026-09-05 06:28:30 | 64 | ||||||||
|
ggraph Resource Report Resource Website 50+ mentions |
ggraph (RRID:SCR_021239) | data processing software, data visualization software, software application, software resource | Software tool as extension of ggplot2 aimed at supporting relational data structures such as networks, graphs, and trees. While it builds upon foundation of ggplot2 and its API it comes with its own self-contained set of geoms, facets, etc., as well as adding concept of layouts to grammar. | Relational data structures support, data networks, data graphs, data trees | is related to: ggplot2 | Free, Available for download, Freely available | https://CRAN.R-project.org/package=ggraph, https://github.com/thomasp85/ggraph/ | SCR_021239 | grammar of graphics for relational data | 2026-09-05 06:29:37 | 53 | ||||||||
|
ggalluvial Resource Report Resource Website 10+ mentions |
ggalluvial (RRID:SCR_021253) | data processing software, data visualization software, software application, software resource | Software tool as ggplot2 extension for alluvial plots. Used to visualize frequency distributions over time or frequency tables involving several categorical variables. Requires user to specify dimensions, either as separate aesthetics or as key-value pairs, relies on separate layers (stats and geoms) to produce strata, alluvia, and alluvial segments called lodes and flows. | Alluvial plots extension, visualize frequency distributions over time, visualize frequency tables involving several categorical variables, |
is listed by: CRAN works with: ggplot2 |
Free, Available for download, Freely available | https://CRAN.R-project.org/package=ggalluvial, https://github.com/corybrunson/ggalluvial/ | SCR_021253 | 2026-09-05 06:29:37 | 18 | |||||||||
|
tidyverse Resource Report Resource Website 100+ mentions |
tidyverse (RRID:SCR_019186) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses. | data science, R package, data analysis, common data representation |
uses: ggplot2 uses: dplyr uses: tidyr is used by: tidySingleCellExperiment is used by: microViz is listed by: CRAN |
Free, Available for download, Freely available | https://www.tidyverse.org/, https://github.com/tidyverse/tidyverse | SCR_019186 | tidyverse 1.3.0 | 2026-09-05 06:28:47 | 259 | ||||||||
|
riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-09-05 06:28:16 | 23 | ||||||||
|
ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps. | visualizing, clustering, multivariate, data, principal, component, analysis, plot, heatmap, bio.tools |
uses: Shiny uses: ggplot2 uses: pheatmap uses: RColorBrewer uses: FactoMineR is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: University of Tartu; Tartu; Estonia |
EFPIA ; Estonian Research Council ; European Commission ; European Federation of Pharmaceutical Industries and Associations ; European Regional Development Fund ; European Union Seventh Framework Programme ; Innovative Medicines Initiative Joint Undertaking |
PMID:25969447 | biotools:clustvis, OMICS_08539 | https://github.com/taunometsalu/ClustVis, https://bio.tools/clustvis | SCR_017133 | 2026-09-05 06:28:19 | 974 | |||||||
|
ggbreak Resource Report Resource Website 1+ mentions |
ggbreak (RRID:SCR_024824) | software resource, software toolkit | Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2. | break down ‘gg’ plot functions, set breakpoints for truncating plot, phylogenetic tree, shrink outlier long branch of phylogenetic tree, |
is listed by: CRAN works with: ggplot2 |
Free, Available for download, Freely available | SCR_024824 | 2026-09-05 06:34:42 | 1 | ||||||||||
|
ggsurvfit Resource Report Resource Website 1+ mentions |
ggsurvfit (RRID:SCR_025045) | software resource, software toolkit | Software R package for flexible time-to-event figures creation. Used to create figures ready for publication. | create figures, figures ready for publication, | works with: ggplot2 | Free, Available for download, Freely available | https://github.com/pharmaverse/ggsurvfit | SCR_025045 | 2026-09-05 06:34:48 | 8 | |||||||||
|
ggvenn Resource Report Resource Website 10+ mentions |
ggvenn (RRID:SCR_025300) | software resource, software toolkit, source code | Software R package to draw venn diagram by ggplot2. | draw venn diagram, | uses: ggplot2 | Free, Available for download, Freely available | SCR_025300 | 2026-09-05 06:34:55 | 41 | ||||||||||
|
forestmodel Resource Report Resource Website 1+ mentions |
forestmodel (RRID:SCR_025250) | software resource, software toolkit, source code | Software R package that produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph(). | forest plots, | uses: ggplot2 | Free, Available for download, Freely available | SCR_025250 | 2026-09-05 06:34:54 | 5 | ||||||||||
|
ggVennDiagram Resource Report Resource Website 10+ mentions |
ggVennDiagram (RRID:SCR_026950) | software resource, software toolkit, source code | Software R package to generate Venn diagram.'ggplot2' implement of Venn Diagram. | generate Venn diagram, | uses: ggplot2 | Fundamental Research Funds for the Central Universities ; National Key Research Program of China ; National Natural Science Foundation of China ; Royal Society-Newton Advanced Fellowship ; Wuhan Applied Foundational Frontier Project |
PMID:34557218 | Free, Available for download, Freely available | https://github.com/gaospecial/ggVennDiagram | SCR_026950 | 2026-09-05 06:35:35 | 46 | |||||||
|
ggbiplot Resource Report Resource Website 10+ mentions |
ggbiplot (RRID:SCR_025581) | software resource, software toolkit, source code | Software R package to provide ggplot2 implementation of biplot, simultaneous plot of scores for observations and vectors for variables for principal component-like analyses. | ggplot2 implementation of biplot, vectors for variables, variables for principal component-like analyses, simultaneous plot of scores, scores for observations, | is related to: ggplot2 | Free, Available for download, Freely available | https://github.com/vqv/ggbiplot | SCR_025581 | 2026-09-05 06:35:02 | 11 | |||||||||
|
ggtext Resource Report Resource Website 1+ mentions |
ggtext (RRID:SCR_026470) | software resource, source code | Software R package that enhances text rendering in ggplot2 by allowing the use of Markdown, HTML, and rich text formatting for annotations, labels, and titles in plots. | Improved text rendering support, ggplot2, annotations, labels, titles, plots | works with: ggplot2 | Free, Available for download, Freely available | https://CRAN.R-project.org/package=ggtext, https://wilkelab.org/ggtext/ | SCR_026470 | 2026-09-05 06:35:23 | 3 | |||||||||
|
ggpointdensity Resource Report Resource Website |
ggpointdensity (RRID:SCR_028856) | software resource, software toolkit, source code | Software R package provides ggplot2 extension that colors scatter plot points by their neighbor count. It solves overplotting in large datasets by showing data density through color while keeping individual points and outliers visible. | color scatter plot points, neighbor count, solve overplotting in large datasets, show data density, | is related to: ggplot2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/ggpointdensity/index.html | SCR_028856 | 2026-09-05 06:36:20 | 0 | |||||||||
|
R Project for Statistical Computing Resource Report Resource Website 10000+ mentions |
R Project for Statistical Computing (RRID:SCR_001905) | R | software resource | Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS. | R software, statistical, computing, graphics, programming, language, bio.tools |
is used by: UTR is used by: MSstats is used by: CummeRbund is used by: deFuse is used by: JASP is used by: Boruta is used by: NMRProcFlow is used by: PlotsOfData is used by: rtransparent is used by: shinyCircoss is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: CRAN is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is related to: Sweave is related to: rOpenSci is related to: R Manuals is related to: Bioconductor is related to: ggplot2 is related to: madsim is related to: Solas is related to: braincog is related to: clustree is related to: PhenoSpD is related to: geomorph is related to: NeuroAnatomy Toolbox is related to: dplyr is related to: glmmADMB is related to: clusterProfiler is related to: ropls is related to: mixOmics is related to: FlowSOM is related to: Rtsne is related to: scran is related to: Rsubread is related to: riboSeqR is related to: Biostrings is related to: riboWaltz is related to: GenomicFeatures is related to: devtools is related to: affy is related to: affydata is related to: Heatmapper is related to: toxprofileR is related to: LTRpred is related to: RaceID is related to: PRSice is related to: Genomic Ranges is related to: Goseq is related to: GAGE is related to: metagear is related to: pagoda2 is related to: dndSCV is related to: tidyr is related to: ClustVis is related to: IDR is related to: NeuroAnatomy Toolbox is related to: rjags is related to: gProfiler2 is related to: knitr is related to: EpiEstim is related to: Minimum-Hypergeometric Test is related to: Network-Based R-Statistics is related to: seqpac is related to: survminer is related to: Vector Generalized Linear and Additive Models is related to: LEA is related to: StAMPP is related to: Betareg is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: Rphenograph is related to: Peptides is related to: taxize is related to: seqinr is related to: reshape2 is related to: monaLisa is related to: mia is related to: Rtsne is related to: R package:stats-package is related to: R package: maxstat is related to: stats |
PMID:18252159 | SCR_021974, nif-0000-10474, OMICS_01147, biotools:r | https://cran.r-project.org/src/base/R-3/, https://bio.tools/r | SCR_001905 | R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing | 2026-09-05 06:24:41 | 52118 |
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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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