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Compare functional enrichment between two experimentally-derived groups of genes or proteins (Peterson, DR., et al.(2018)) <doi:10.1371/journal.pone.0198139>. Given a list of gene symbols, 'diffEnrich' will perform differential enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. This package provides a number of functions that are intended to be used in a pipeline. Briefly, the user provides a KEGG formatted species id for either human, mouse or rat, and the package will download and clean species specific ENTREZ gene IDs and map them to their respective KEGG pathways by accessing KEGG's REST API. KEGG's API is used to guarantee the most up-to-date pathway data from KEGG. Next, the user will identify significantly enriched pathways from two gene sets, and finally, the user will identify pathways that are differentially enriched between the two gene sets. In addition to the analysis pipeline, this package also provides a plotting function.
| Version: | 0.1.2 |
| Depends: | dplyr, ggplot2, R (≥ 2.10) |
| Imports: | here, stats, rlang, stringr, reshape2, ggnewscale |
| Suggests: | knitr, rmarkdown, kableExtra, diagram |
| Published: | 2022-06-27 |
| DOI: | 10.32614/CRAN.package.diffEnrich |
| Author: | Harry Smith [aut, cre], Laura Saba [aut] |
| Maintainer: | Harry Smith <harry.smith at ucdenver.edu> |
| BugReports: | https://github.com/SabaLab/diffEnrich/issues |
| License: | GPL-2 |
| URL: | https://github.com/SabaLab/diffEnrich |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | diffEnrich results |
| Reference manual: | diffEnrich.pdf |
| Vignettes: |
diffEnrich by example |
| Package source: | diffEnrich_0.1.2.tar.gz |
| Windows binaries: | r-devel: diffEnrich_0.1.2.zip, r-release: diffEnrich_0.1.2.zip, r-oldrel: diffEnrich_0.1.2.zip |
| macOS binaries: | r-release (arm64): diffEnrich_0.1.2.tgz, r-oldrel (arm64): diffEnrich_0.1.2.tgz, r-release (x86_64): diffEnrich_0.1.2.tgz, r-oldrel (x86_64): diffEnrich_0.1.2.tgz |
| Old sources: | diffEnrich archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.