In w-korani/keggseq: KEGG analysis and visualizing of differentially expressed genes

%\VignetteEngine{knitr::knitr} %\VignetteIndexEntry{keggseq}

keggseq:

The package 'keggseq' was developed to apply KEGG enrichment analysis mainly for ployploids utilizing their sub-genomes. keggseq provides some advantages over the available tools: 1. It allows applying KEGG enrichment analysis for diploids or ployploids with any levels of gene duplications.

1. It generates ready-to-published graphs.

2. It produces graphs of interested pathways that have differentially expressed enzymes marked.

3. It generates csv files containing detailed information of enzymes included in the interested pathways.

4. It allows correcting genes IDs if the user wants to use annotation different from Kyoto Encyclopedia of Genes and Genomes annotation.

5. It is a run-time package since the data is downloaded directly from Kyoto Encyclopedia of Genes and Genomes database so it does not require an internal database for specific species.

6. It is step-by-step and easy to be implemented.

Citation

The publication will be published soon

Installation:

devtools::install_github("w-korani/keggseq")

keggseq_manual.pdf file contains detail information of function using

w-korani/keggseq documentation built on May 3, 2019, 7:10 p.m.