Package: GOsummaries 2.14.0

Raivo Kolde

GOsummaries: Word cloud summaries of GO enrichment analysis

A package to visualise Gene Ontology (GO) enrichment analysis results on gene lists arising from different analyses such clustering or PCA. The significant GO categories are visualised as word clouds that can be combined with different plots summarising the underlying data.

Authors:Raivo Kolde <[email protected]>

GOsummaries_2.14.0.tar.gz
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GOsummaries.pdf |GOsummaries.html✨
GOsummaries/json (API)
NEWS

# Install 'GOsummaries' in R:

install.packages('GOsummaries', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/raivokolde/gosummaries/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

gs_kmeans - Example gene expression dataset
gs_limma - Example gene expression dataset
gs_limma_exp - Example gene expression dataset
gs_pca - Example gene expression dataset
metabolomic_example - Example metabolomic dataset
metagenomic_example - Example metagenomic dataset
tissue_example - Example gene expression dataset

On CRAN:

geneexpression clustering go visualization

3.77 score 11 stars 36 scripts 38 downloads 12 exports 38 dependencies

Last updated 7 years agofrom:a999564173. Checks:ERROR: 1 WARNING: 8. Indexed: no.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 02 2024
R-4.5-win-x86_64	WARNING	Nov 02 2024
R-4.5-linux-x86_64	WARNING	Nov 02 2024
R-4.4-win-x86_64	WARNING	Nov 02 2024
R-4.4-mac-x86_64	WARNING	Nov 02 2024
R-4.4-mac-aarch64	WARNING	Nov 02 2024
R-4.3-win-x86_64	WARNING	Nov 02 2024
R-4.3-mac-x86_64	WARNING	Nov 02 2024
R-4.3-mac-aarch64	WARNING	Nov 02 2024

Exports:add_expression.gosummaries add_to_slot.gosummaries customize gosummaries is.gosummaries panel_boxplot panel_boxplot_classes panel_violin panel_violin_box panel_violin_box_classes panel_violin_classes plotWordcloud

Dependencies:bitops cli colorspace fansi farver ggplot2 glue gProfileR gtable isoband labeling lattice lifecycle limma magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr R6 RColorBrewer Rcpp RCurl reshape2 rlang scales statmod stringi stringr tibble utf8 vctrs viridisLite withr

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Word cloud summaries of GO enrichment analysis	GOsummaries-package GOsummaries
Add expression data to gosummaries object	add_expression.gosummaries
Customization function for panel	customize
Constructor for gosummaries object	gosummaries gosummaries.default
Prepare gosummaries object based on k-means results	gosummaries.kmeans
Prepare gosummaries object based on limma results	gosummaries.MArrayLM
Prepare gosummaries object based on Multi Dimensional Scaling (MDS) results	gosummaries.matrix
Prepare gosummaries object based on PCA results	gosummaries.prcomp
Functions for working with gosummaries object	add_to_slot.gosummaries is.gosummaries print.gosummaries [.gosummaries
Example metabolomic dataset	metabolomic_example
Example metagenomic dataset	metagenomic_example
Panel drawing functions	panel_boxplot panel_boxplot_classes panel_violin panel_violin_box panel_violin_box_classes panel_violin_classes
Plot the GOsummaries figure	plot.gosummaries
Plot a wordcloud given words and frequencies	plotWordcloud
Example gene expression dataset	gs_kmeans gs_limma gs_limma_exp gs_pca tissue_example