StarBioTrek: StarBioTrek

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

Author
Claudia Cava, Isabella Castiglioni
Date of publication
None
Maintainer
Claudia Cava <claudia.cava@ibfm.cnr.it>
License
GPL (>= 3)
Version
1.0.0
URLs

View on Bioconductor

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 network data in order to...
list_path_plot
A matrix of gene expression for pathways given by the user.
netw
network data
norm
TCGA data with normal samples
path
Pathway data from KEGG
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

Files in this package

StarBioTrek/DESCRIPTION
StarBioTrek/NAMESPACE
StarBioTrek/NEWS
StarBioTrek/R
StarBioTrek/R/StarBioTrek.r
StarBioTrek/R/getdata.R
StarBioTrek/R/internal.R
StarBioTrek/R/path_star.R
StarBioTrek/README.md
StarBioTrek/build
StarBioTrek/build/vignette.rds
StarBioTrek/data
StarBioTrek/data/Data_CANCER_normUQ_filt.rda
StarBioTrek/data/datalist
StarBioTrek/data/list_path_plot.rda
StarBioTrek/data/netw.rda
StarBioTrek/data/norm.rda
StarBioTrek/data/path.rda
StarBioTrek/data/score_euc_dist.rda
StarBioTrek/data/tumo.rda
StarBioTrek/inst
StarBioTrek/inst/CITATION
StarBioTrek/inst/doc
StarBioTrek/inst/doc/StarBioTrek.R
StarBioTrek/inst/doc/StarBioTrek.Rmd
StarBioTrek/inst/doc/StarBioTrek.html
StarBioTrek/inst/doc/StarBioTrek_Application_Examples.R
StarBioTrek/inst/doc/StarBioTrek_Application_Examples.Rmd
StarBioTrek/inst/doc/StarBioTrek_Application_Examples.pdf
StarBioTrek/man
StarBioTrek/man/Data_CANCER_normUQ_filt.Rd
StarBioTrek/man/GE_matrix.Rd
StarBioTrek/man/SelectedSample.Rd
StarBioTrek/man/StarBioTrek.Rd
StarBioTrek/man/average.Rd
StarBioTrek/man/ds_score_crtlk.Rd
StarBioTrek/man/euc_dist_crtlk.Rd
StarBioTrek/man/getKEGGdata.Rd
StarBioTrek/man/getNETdata.Rd
StarBioTrek/man/list_path_net.Rd
StarBioTrek/man/list_path_plot.Rd
StarBioTrek/man/netw.Rd
StarBioTrek/man/norm.Rd
StarBioTrek/man/path.Rd
StarBioTrek/man/plotting_cross_talk.Rd
StarBioTrek/man/proc_path.Rd
StarBioTrek/man/process_matrix.Rd
StarBioTrek/man/score_euc_dist.Rd
StarBioTrek/man/select_class.Rd
StarBioTrek/man/st_dv.Rd
StarBioTrek/man/svm_classification.Rd
StarBioTrek/man/tumo.Rd
StarBioTrek/vignettes
StarBioTrek/vignettes/StarBioTrek.Rmd
StarBioTrek/vignettes/StarBioTrek_Application_Examples.Rmd
StarBioTrek/vignettes/plot_path.png