StarBioTrek: StarBioTrek
Version 1.2.0

This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.

AuthorClaudia Cava, Isabella Castiglioni
Bioconductor views GeneRegulation KEGG Network Pathways
Date of publicationNone
MaintainerClaudia Cava <claudia.cava@ibfm.cnr.it>
LicenseGPL (>= 3)
Version1.2.0
URL https://github.com/claudiacava/StarBioTrek
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("StarBioTrek")

Getting started

README.md
StarBioTrek:Application Examples"
Working with StarBioTrek package"

Popular man pages

GE_matrix: Get human KEGG pathway data and a gene expression matrix in...
list_path_net: Get human KEGG pathway data and output of path_net in order...
matrix_plot: Get human KEGG pathway data and a gene expression matrix in...
netw: network data
path: Pathway data from KEGG
process_matrix: Process matrix TCGA data after the selection of pairwise...
st_dv: For TCGA data get human pathway data and creates a measure of...
See all...

All man pages Function index File listing

Man pages

average: For TCGA data get human pathway data and creates a matrix...
Data_CANCER_normUQ_filt: TCGA data
ds_score_crtlk: For TCGA data get human pathway data and creates a measure of...
euc_dist_crtlk: For TCGA data get human pathway data and creates a measure of...
GE_matrix: Get human KEGG pathway data and a gene expression matrix in...
getKEGGdata: Get human KEGG pathway data.
getNETdata: Get network data.
list_path_net: Get human KEGG pathway data and output of path_net in order...
list_path_plot: A matrix of gene expression for pathways given by the user.
matrix_plot: Get human KEGG pathway data and a gene expression matrix in...
netw: network data
norm: TCGA data with normal samples
path: Pathway data from KEGG
path_net: Get human KEGG pathway data and network data in order to...
plotting_cross_talk: Get human KEGG pathway data and a gene expression matrix we...
process_matrix: Process matrix TCGA data after the selection of pairwise...
proc_path: Get human KEGG pathway data.
score_euc_dist: Score Matrix of pairwise pathway using euclidean distance
select_class: Select the class of TCGA data
SelectedSample: Select the class of TCGA data
StarBioTrek: Download data
st_dv: For TCGA data get human pathway data and creates a measure of...
svm_classification: SVM classification for each feature
tumo: TCGA data with tumour samples

Functions

Data_CANCER_normUQ_filt Man page
GE_matrix Man page Source code
SelectedSample Man page Source code
StarBioTrek Man page
StarBioTrek-package Man page
average Man page Source code
ds_score_crtlk Man page Source code
euc_dist_crtlk Man page Source code
getKEGGdata Man page Source code
getNETdata Man page Source code
list_path_net Man page Source code
list_path_plot Man page
matrix_plot Man page Source code
netw Man page
norm Man page
path Man page
path_net Man page Source code
plotting_cross_talk Man page Source code
proc_path Man page Source code
process_matrix Man page Source code
process_matrix_cell_process Source code
score_euc_dist Man page
select_class Man page Source code
select_path_amn Source code
select_path_carb Source code
select_path_cell_comm Source code
select_path_cell_grow Source code
select_path_circ_syst Source code
select_path_cofa Source code
select_path_dig_syst Source code
select_path_en Source code
select_path_end_syst Source code
select_path_exc_syst Source code
select_path_fold Source code
select_path_gly Source code
select_path_imm_syst Source code
select_path_lip Source code
select_path_ner_syst Source code
select_path_repl Source code
select_path_sens_syst Source code
select_path_sign Source code
select_path_sign_mol Source code
select_path_transc Source code
select_path_transl Source code
select_path_transp_ca Source code
st_dv Man page Source code
svm_classification Man page Source code
tumo Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/StarBioTrek.r
R/getdata.R
R/internal.R
R/path_star.R
README.md
build
build/vignette.rds
data
data/Data_CANCER_normUQ_filt.rda
data/datalist
data/list_path_plot.rda
data/netw.rda
data/norm.rda
data/path.rda
data/score_euc_dist.rda
data/tumo.rda
inst
inst/CITATION
inst/doc
inst/doc/StarBioTrek.R
inst/doc/StarBioTrek.Rmd
inst/doc/StarBioTrek.html
inst/doc/StarBioTrek_Application_Examples.R
inst/doc/StarBioTrek_Application_Examples.Rmd
inst/doc/StarBioTrek_Application_Examples.pdf
man
man/Data_CANCER_normUQ_filt.Rd
man/GE_matrix.Rd
man/SelectedSample.Rd
man/StarBioTrek.Rd
man/average.Rd
man/ds_score_crtlk.Rd
man/euc_dist_crtlk.Rd
man/getKEGGdata.Rd
man/getNETdata.Rd
man/list_path_net.Rd
man/list_path_plot.Rd
man/matrix_plot.Rd
man/netw.Rd
man/norm.Rd
man/path.Rd
man/path_net.Rd
man/plotting_cross_talk.Rd
man/proc_path.Rd
man/process_matrix.Rd
man/score_euc_dist.Rd
man/select_class.Rd
man/st_dv.Rd
man/svm_classification.Rd
man/tumo.Rd
vignettes
vignettes/StarBioTrek.Rmd
vignettes/StarBioTrek_Application_Examples.Rmd
vignettes/plot_path.png
StarBioTrek documentation built on May 20, 2017, 10:43 p.m.