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diffEnrich  

Given a List of Gene Symbols, Performs Differential Enrichment Analysis
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]
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.
Previous versions and publish date:
0.1.0 (2019-11-01 23:20), 0.1.1 (2019-11-21 23:40)
Other packages that cited diffEnrich R package
View diffEnrich citation profile
Other R packages that diffEnrich depends, 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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