Package: PAVER 0.0.0.9000

William G Ryan V

PAVER: PAVER: Pathway Analysis Visualization with Embedding Representations

Summary visualization using embedding representations to reveal underlying themes within sets of pathway terms.

Authors:William G Ryan V [aut, cre]

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PAVER.pdf |PAVER.html✨
PAVER/json (API)

# Install 'PAVER' in R:

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

Bug tracker:https://github.com/cogdisreslab/paver/issues

Datasets:

gsea_example - An example of GSEA results
kegg_example - An example of KEGG results

On CRAN:

3.65 score 6 scripts 8 exports 163 dependencies

Last updated 4 months agofrom:9b74c6403f. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 02 2024
R-4.5-win	NOTE	Nov 02 2024
R-4.5-linux	NOTE	Nov 02 2024
R-4.4-win	NOTE	Nov 02 2024
R-4.4-mac	NOTE	Nov 02 2024
R-4.3-win	NOTE	Nov 02 2024
R-4.3-mac	NOTE	Nov 02 2024

Exports:generate_themes PAVER_combined_plot PAVER_export PAVER_hunter_plot PAVER_interpretation_plot PAVER_regulation_plot PAVER_theme_plot prepare_data

Dependencies:abind askpass backports base64enc BiocGenerics bit bit64 boot broom bslib cachem car carData checkmate circlize class cli clipr clue cluster codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon curl data.table Deriv digest doBy doParallel dplyr dynamicTreeCut e1071 ellipse evaluate fansi farver fastmap fontawesome forcats foreach foreign Formula fs gdata generics GetoptLong ggplot2 ggplotify ggprism ggpubr ggrepel ggsci ggsignif glmnet GlobalOptions glue gridExtra gridGraphics gtable gtools haven here highr Hmisc hms htmlTable htmltools htmlwidgets IRanges isoband iterators jomo jquerylib jsonlite knitr labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels matrixStats memoise mgcv mice microbenchmark mime minqa mitml modelr munsell nlme nloptr nnet nnls numDeriv openssl ordinal pan pbkrtest pillar pkgconfig plotrix png polynom prettyunits progress proxy purrr quantreg R6 randomcoloR rappdirs RColorBrewer Rcpp RcppEigen RcppTOML readr reticulate rjson rlang rmarkdown rpart rprojroot RSpectra rstatix rstudioapi Rtsne S4Vectors sass scales shape smacof SparseM stringi stringr survival sys tibble tidyr tidyselect tinytex tzdb ucminf umap utf8 V8 vctrs viridis viridisLite vroom weights withr wordcloud xfun yaml yulab.utils

PAVER

Rendered fromPAVER.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2024-07-12
Started: 2023-04-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute Cosine Dissimilarity Matrix	cosine_dissimilarity
Cluster pathway embeddings and generate themes	generate_themes
An example of GSEA results	gsea_example
An example of KEGG results	kegg_example
PAVER_combined_plot	PAVER_combined_plot
Export PAVER results to a formatted data frame	PAVER_export
PAVER_hunter_plot	PAVER_hunter_plot
PAVER_interpretation_plot	PAVER_interpretation_plot
PAVER_regulation_plot	PAVER_regulation_plot
PAVER_theme_plot	PAVER_theme_plot
Prepare pathway analysis results for downstream theme generation and summary visualization	prepare_data

Usage by other packages (reverse dependencies)