Package: GOCompare 1.0.2.1

Chrystian Camilo Sosa

GOCompare: Comprehensive GO Terms Comparison Between Species

Supports the assessment of functional enrichment analyses obtained for several lists of genes and provides a workflow to analyze them between two species via weighted graphs. Methods are described in Sosa et al. (2023) <doi:10.1016/j.ygeno.2022.110528>.

Authors:Chrystian Camilo Sosa [aut, cre, cph], Diana Carolina Clavijo-Buriticá [aut], Mauricio Alberto Quimbaya [aut], Maria Victoria Diaz [ctb], Camila Riccio Rengifo [ctb], Nicolas López-Rozo [ctb], Victor Hugo García Merchán [aut, ctb], Arlen James Mosquera [ctb], Andrés Álvarez [ctb]

GOCompare_1.0.2.1.tar.gz
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GOCompare_1.0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GOCompare/json (API)

# Install 'GOCompare' in R:
install.packages('GOCompare', repos = c('https://ccsosa.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ccsosa/gocompare/issues

Datasets:
  • A_thaliana - A thaliana functional enrichment analysis of 2224 ortholog genes related to cancer-hallmarks
  • A_thaliana_compress - A thaliana functional enrichment analysis results for "AID","DCE","RCD","SPS" cancer-hallmarks
  • comparison_ex_compress - Functional enrichment analysis comparison between H. sapiens and A. thaliana for "AID","DCE","RCD","SPS" cancer-hallmarks
  • comparison_ex_compress_CH - Functional enrichment analysis comparison between H. sapiens and A. thaliana for "DCE", and "RCD" cancer-hallmarks. This dataset contains 10 GO terms per category to allow a fast run of the function graph_two_GOspecies.
  • H_sapiens - H. sapiens functional enrichment analysis of 5494 genes related to cancer-hallmarks
  • H_sapiens_compress - H. sapiens functional enrichment analysis results for "AID","DCE","RCD","SPS" cancer-hallmarks

On CRAN:

Conda:

3.78 score 12 stars 1 scripts 363 downloads 6 exports 35 dependencies

Last updated from:e306e01762. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE183
source / vignettesOK244
linux-releaseNOTE202
macos-releaseNOTE154
macos-oldrelNOTE193
windows-develNOTE111
windows-releaseNOTE105
windows-oldrelNOTE125
wasm-releaseOK115

Exports:compareGOspeciesevaluateCAT_speciesevaluateGO_speciesgraph_two_GOspeciesgraphGOspeciesmostFrequentGOs

Dependencies:apecliclustercpp11digestfarverggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSmathjaxrMatrixmgcvnlmepermutepkgconfigR6RColorBrewerRcpprlangS7scalesstringistringrvctrsveganviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
GOCompare: An R package to compare GO terms of gene lists (categories) and their orthologsGOCompare-package GOCompare
A thaliana functional enrichment analysis of 2224 ortholog genes related to cancer-hallmarksA_thaliana
A thaliana functional enrichment analysis results for "AID","DCE","RCD","SPS" cancer-hallmarksA_thaliana_compress
Visual representation for the results of functional enrichment analysis to compare two species and a series of categoriescompareGOspecies
Functional enrichment analysis comparison between H. sapiens and A. thaliana for "AID","DCE","RCD","SPS" cancer-hallmarkscomparison_ex_compress
Functional enrichment analysis comparison between H. sapiens and A. thaliana for "DCE", and "RCD" cancer-hallmarks. This dataset contains 10 GO terms per category to allow a fast run of the function graph_two_GOspecies.comparison_ex_compress_CH
Comprehensive comparison between species using categories and Pearson's Chi-squared TestsevaluateCAT_species
Comprehensive comparison between species using GO terms and Pearson's Chi-squared TestsevaluateGO_species
Undirected network representation for the results of functional enrichment analysis to compare two species and a series of categoriesgraph_two_GOspecies
Undirected network representation for the results of functional enrichment analysis for one speciesgraphGOspecies
H. sapiens functional enrichment analysis of 5494 genes related to cancer-hallmarksH_sapiens
H. sapiens functional enrichment analysis results for "AID","DCE","RCD","SPS" cancer-hallmarksH_sapiens_compress
Most frequent GO terms among groups for a data.framemostFrequentGOs