GOsummaries: Word cloud summaries of GO enrichment analysis
Version 2.10.0

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.

AuthorRaivo Kolde <raivo.kolde@eesti.ee>
Bioconductor views Clustering GO GeneExpression Visualization
Date of publicationNone
MaintainerRaivo Kolde <raivo.kolde@eesti.ee>
LicenseGPL (>= 2)
Version2.10.0
URL https://github.com/raivokolde/GOsummaries
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GOsummaries")

Getting started

Package overview
README.md

Popular man pages

add_to_slot.gosummaries: Functions for working with gosummaries object
customize: Customization function for panel
GOsummaries-package: Word cloud summaries of GO enrichment analysis
metabolomic_example: Example metabolomic dataset
metagenomic_example: Example metagenomic dataset
plot.gosummaries: Plot the GOsummaries figure
plotWordcloud: Plot a wordcloud given words and frequencies
See all...

All man pages Function index File listing

Man pages

add_expression.gosummaries: Add expression data to gosummaries object
add_to_slot.gosummaries: Functions for working with gosummaries object
customize: Customization function for panel
gosummaries: Constructor for gosummaries object
gosummaries.kmeans: Prepare gosummaries object based on k-means results
gosummaries.MArrayLM: Prepare gosummaries object based on limma results
gosummaries.matrix: Prepare gosummaries object based on Multi Dimensional Scaling...
GOsummaries-package: Word cloud summaries of GO enrichment analysis
gosummaries.prcomp: Prepare gosummaries object based on PCA results
metabolomic_example: Example metabolomic dataset
metagenomic_example: Example metagenomic dataset
panel_boxplot: Panel drawing functions
plot.gosummaries: Plot the GOsummaries figure
plotWordcloud: Plot a wordcloud given words and frequencies
tissue_example: Example gene expression dataset

Functions

GOsummaries Man page
GOsummaries-package Man page
[.gosummaries Man page
add_dummydata.gosummaries Source code
add_expression.gosummaries Man page Source code
add_pca.gosummaries Source code
add_to_slot.gosummaries Man page Source code
adjust_wordcloud_appearance Source code
annotate.gosummaries Source code
calc_component_dimensions Source code
calc_components_dimensions Source code
combine_classes Source code
convert_gene_ids Source code
convert_scores Source code
customize Man page Source code
customize_dummy Source code
drawDetails.zeroGrob Source code
dummyData Source code
filter_gprofiler Source code
filter_pca_wc_data Source code
filter_wc_data Source code
findCoordinates Source code
findCoordinates_left Source code
findCoordinates_left_top Source code
gen_legend Source code
gen_wordcloud_legend Source code
gosummaries Man page Source code
gosummaries.MArrayLM Man page Source code
gosummaries.default Man page Source code
gosummaries.kmeans Man page Source code
gosummaries.matrix Man page Source code
gosummaries.prcomp Man page Source code
gosummaries_base Source code
gs_kmeans Man page
gs_limma Man page
gs_limma_exp Man page
gs_pca Man page
is.dummyData Source code
is.gosummaries Man page Source code
is.zero Source code
metabolomic_example Man page
metagenomic_example Man page
open_file_con Source code
padz Source code
panel_boxplot Man page Source code
panel_boxplot_classes Man page Source code
panel_dummy Source code
panel_histogram Source code
panel_violin Man page Source code
panel_violin_box Man page Source code
panel_violin_box_classes Man page Source code
panel_violin_classes Man page Source code
panelize_ggplot2 Source code
plot.gosummaries Man page Source code
plotWordcloud Man page Source code
plot_arrow Source code
plot_component Source code
plot_motor Source code
plot_wordcloud Source code
print.gosummaries Man page Source code
pspearman Source code
shorten_strings Source code
spearman_mds Source code
tissue_example Man page
zeroGrob Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GOsummaries-package.R
R/GOsummaries.R
R/exampleDatasets.R
R/wordcloud.R
README.md
build
build/vignette.rds
data
data/datalist
data/gs_kmeans.rda
data/gs_limma.rda
data/gs_limma_exp.rda
data/gs_pca.rda
data/metabolomic_example.RData
data/metagenomic_example.RData
data/tissue_example.RData
inst
inst/CITATION
inst/doc
inst/doc/GOsummaries-basics.R
inst/doc/GOsummaries-basics.Rnw
inst/doc/GOsummaries-basics.pdf
man
man/GOsummaries-package.Rd
man/add_expression.gosummaries.Rd
man/add_to_slot.gosummaries.Rd
man/customize.Rd
man/gosummaries.MArrayLM.Rd
man/gosummaries.Rd
man/gosummaries.kmeans.Rd
man/gosummaries.matrix.Rd
man/gosummaries.prcomp.Rd
man/metabolomic_example.Rd
man/metagenomic_example.Rd
man/panel_boxplot.Rd
man/plot.gosummaries.Rd
man/plotWordcloud.Rd
man/tissue_example.Rd
src
src/Makevars
src/Makevars.win
src/findCoordinates.cpp
vignettes
vignettes/GOsummaries-basics.Rnw
vignettes/GS.pdf
GOsummaries documentation built on May 20, 2017, 10:54 p.m.

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