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diffEnrich
View on CRAN: Click
here
Download and install diffEnrich package within the R console
Install from CRAN:
install.packages("diffEnrich")
Install from Github:
library("remotes")
install_github("cran/diffEnrich")
Install by package version:
library("remotes")
install_version("diffEnrich", "0.1.2")
Attach the package and use:
library("diffEnrich")
Maintained by
Harry Smith
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-11-01
Latest Update: 2022-06-27
Description:
Compare functional enrichment between two experimentally-derived groups of genes or proteins (Peterson, DR., et al.(2018)) . 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.
How to cite:
Harry Smith (2019). diffEnrich: Given a List of Gene Symbols, Performs Differential Enrichment Analysis. R package version 0.1.2, https://cran.r-project.org/web/packages/diffEnrich. Accessed 22 Dec. 2024.
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imports, suggests or enhances
Complete documentation for diffEnrich
Functions, R codes and Examples using
the diffEnrich R package
Some associated functions: diffEnrich . dot-api_pull . dot-combineEnrich . dot-data_read . geneLists . get_kegg . kegg . pathEnrich . plotFoldEnrichment .
Some associated R codes: diffEnrich.R . get_kegg.R . pathEnrich.R . plotFoldEnrichment.R . sample_data.R . Full diffEnrich package functions and examples
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