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'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

12 exports 11 stars 1.38 score 38 dependencies 23 downloads

Last updated 6 years agofrom:a999564173

Exports:add_expression.gosummariesadd_to_slot.gosummariescustomizegosummariesis.gosummariespanel_boxplotpanel_boxplot_classespanel_violinpanel_violin_boxpanel_violin_box_classespanel_violin_classesplotWordcloud

Dependencies:bitopsclicolorspacefansifarverggplot2gluegProfileRgtableisobandlabelinglatticelifecyclelimmamagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppRCurlreshape2rlangscalesstatmodstringistringrtibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Word cloud summaries of GO enrichment analysisGOsummaries-package GOsummaries
Add expression data to gosummaries objectadd_expression.gosummaries
Customization function for panelcustomize
Constructor for gosummaries objectgosummaries gosummaries.default
Prepare gosummaries object based on k-means resultsgosummaries.kmeans
Prepare gosummaries object based on limma resultsgosummaries.MArrayLM
Prepare gosummaries object based on Multi Dimensional Scaling (MDS) resultsgosummaries.matrix
Prepare gosummaries object based on PCA resultsgosummaries.prcomp
Functions for working with gosummaries objectadd_to_slot.gosummaries is.gosummaries print.gosummaries [.gosummaries
Example metabolomic datasetmetabolomic_example
Example metagenomic datasetmetagenomic_example
Panel drawing functionspanel_boxplot panel_boxplot_classes panel_violin panel_violin_box panel_violin_box_classes panel_violin_classes
Plot the GOsummaries figureplot.gosummaries
Plot a wordcloud given words and frequenciesplotWordcloud
Example gene expression datasetgs_kmeans gs_limma gs_limma_exp gs_pca tissue_example