KEGGprofile: An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway

KEGGprofile is an annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. KEGGprofile facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples.

Author
Shilin Zhao, Yan Guo, Yu Shyr
Date of publication
None
Maintainer
Shilin Zhao <shilin.zhao@vanderbilt.edu>
License
GPL (>= 2)
Version
1.16.0

View on Bioconductor

Man pages

col_by_value
col_by_value
convertId
convertId
download_KEGGfile
download_KEGGfile
download_latest_pathway
download_latest_pathway
find_enriched_pathway
find_enriched_pathway
newIdMatrix
newIdMatrix
parse_XMLfile
parse_XMLfile
pho_sites_count
number of phosphorylation sites quantified for each gene
plot_pathway
plot_pathway
plot_pathway_cor
plot_pathway_cor
plot_profile
plot_profile
pro_pho_expr
expression profiles in proteome and phosphoproteome

Files in this package

KEGGprofile/DESCRIPTION
KEGGprofile/NAMESPACE
KEGGprofile/NEWS
KEGGprofile/R
KEGGprofile/R/KEGG_function.R
KEGGprofile/R/convertId.R
KEGGprofile/README.md
KEGGprofile/build
KEGGprofile/build/vignette.rds
KEGGprofile/data
KEGGprofile/data/pho_sites_count.rda
KEGGprofile/data/pro_pho_expr.rda
KEGGprofile/inst
KEGGprofile/inst/doc
KEGGprofile/inst/doc/KEGGprofile.R
KEGGprofile/inst/doc/KEGGprofile.Rnw
KEGGprofile/inst/doc/KEGGprofile.pdf
KEGGprofile/inst/doc/Ref.bib
KEGGprofile/inst/extdata
KEGGprofile/inst/extdata/hsa04110.png
KEGGprofile/inst/extdata/hsa04110.xml
KEGGprofile/man
KEGGprofile/man/col_by_value.Rd
KEGGprofile/man/convertId.Rd
KEGGprofile/man/download_KEGGfile.Rd
KEGGprofile/man/download_latest_pathway.Rd
KEGGprofile/man/find_enriched_pathway.Rd
KEGGprofile/man/newIdMatrix.Rd
KEGGprofile/man/parse_XMLfile.Rd
KEGGprofile/man/pho_sites_count.Rd
KEGGprofile/man/plot_pathway.Rd
KEGGprofile/man/plot_pathway_cor.Rd
KEGGprofile/man/plot_profile.Rd
KEGGprofile/man/pro_pho_expr.Rd
KEGGprofile/vignettes
KEGGprofile/vignettes/KEGGprofile.Rnw
KEGGprofile/vignettes/Ref.bib