Package: Paralogs 0.2.1

Paralogs: Visualizing Differential Expression of Paralogs in KEGG Gene Pathways

This package provides functions to visualize the differential expression of paralogs in KEGG gene pathways. The package includes functions to download KEGG gene pathways, extract paralogs from the pathways, and visualize the differential expression of the paralogs. The package also includes functions to visualize the expression of paralogs in the context of the KEGG gene pathways.

Authors:Carson Stacy [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Paralogs/json (API)

# Install 'Paralogs' in R:

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

Bug tracker:https://github.com/clstacy/paralogs/issues

Datasets:

example_enrich_results - An example output of enrichKEGG is provided in the 'example_enrich_results' dataset. The results are the top enrichments for the genes in the lrt_yeast example. This data is used in vignette examples.
lrt_yeast - An example DGELRT object is provided in the 'lrt_yeast' dataset. This object contains the results of a differential gene expression analysis using the edgeR package. logFC values correspond to the effect of a gene knockout on response to ethanol stress in yeast.

On CRAN:

2.70 score 1 stars 4 scripts 9 exports 107 dependencies

Last updated from:7c1ba2bfc1. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	233
source / vignettes	OK	255
linux-release-x86_64	WARNING	230
macos-release-arm64	WARNING	157
macos-oldrel-arm64	WARNING	136
windows-devel	WARNING	167
windows-release	WARNING	192
windows-oldrel	WARNING	169
wasm-release	OK	146

Exports:%>%create_ggkegg createParalogPlots fetchKeggReactions getPathwayNumber loadEnrichResults loadGeneData plotParalogs process_ggkegg

Dependencies:AnnotationDbi askpass base64enc Biobase BiocFileCache BiocGenerics Biostrings bit bit64 blob bslib cachem cli cpp11 crayon curl data.table DBI dbplyr digest dplyr edgeR evaluate farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggforce ggiraph ggkegg ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle limma locfit magick magrittr MASS Matrix memoise mime openssl patchwork pillar pkgconfig png polyclip purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown RSQLite S4Vectors S7 sass scales Seqinfo shadowtext statmod stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tinytex tweenr utf8 vctrs viridis viridisLite withr xfun XML XVector yaml

my-vignette

Rendered frommy-vignette.Rmdusingknitr::rmarkdown

Last update: 2024-05-16
Started: 2024-05-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create ggkegg Object for KEGG Pathway Visualization	create_ggkegg
Create KEGG Pathway Graphs	createParalogPlots
An example output of enrichKEGG is provided in the `example_enrich_results` dataset. The results are the top enrichments for the genes in the lrt_yeast example. This data is used in vignette examples.	example_enrich_results
Fetch KEGG Reactions	fetchKeggReactions
Get Pathway Number to match row of enrichKEGG to KEGG pathway of interest	getPathwayNumber
load Input data (enrichKEGG object)	loadEnrichResults
load Input data (enrichKEGG object)	loadGeneData
An example DGELRT object is provided in the `lrt_yeast` dataset. This object contains the results of a differential gene expression analysis using the edgeR package. logFC values correspond to the effect of a gene knockout on response to ethanol stress in yeast.	lrt_yeast
Full Workflow for KEGG Pathway Visualization	plotParalogs
Process ggkegg Data for Visualization	process_ggkegg