CancerSubtypes: Cancer subtypes identification, validation and visualization based on genomic data

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CancerSubtypes integrates the current common computational biology methods for cancer subtypes identification and provides a standardized framework for cancer subtype analysis based on the genomic datasets.

Author
Taosheng Xu<taosheng.x@gmail.com>, Thuc Le<Thuc.Le@unisa.edu.au>
Date of publication
None
Maintainer
Taosheng Xu<taosheng.x@gmail.com>
License
GPL (>= 2)
Version
1.0.0

View on Bioconductor

Man pages

data.checkDistribution
Data check distribution
data.imputation
Data imputation
data.normalization
Data normalization
DiffExp.limma
DiffExp.limma
drawHeatmap
Generate heatmaps
ExecuteCC
Execute Consensus Clustering
ExecuteCNMF
Execute Consensus NMF (Nonnegative matrix factorization)
ExecuteiCluster
Execute iCluster (Integrative clustering of multiple genomic...
ExecuteSNF
Execute SNF(Similarity Network Fusion )
ExecuteSNF.CC
Execute the combined SNF (Similarity Network Fusion) and...
FSbyCox
Biological feature (such as gene) selection based on Cox...
FSbyMAD
Biological feature (such as gene) selection based on the most...
FSbyPCA
Biological feature (such as gene) dimension reduction and...
FSbyVar
Biological feature (such as gene) selection based on the most...
GeneExp
Dataset: Gene expression
miRNAExp
Dataset: miRNA expression
saveFigure
This function save the figure in the current plot.
sigclustTest
A statistical method for testing the significance of...
silhouette_SimilarityMatrix
Compute or Extract Silhouette Information from Clustering...
spectralAlg
This is an internal function but need to be exported for the...
status
Dataset: Survival status
survAnalysis
Survival analysis(Survival curves, Log-rank test) and compute...
time
Dataset: Survival time

Files in this package

CancerSubtypes/CancerSubtypes.Rproj
CancerSubtypes/DESCRIPTION
CancerSubtypes/NAMESPACE
CancerSubtypes/R
CancerSubtypes/R/ClusteringMethod.R
CancerSubtypes/R/DataProcess.R
CancerSubtypes/R/Valiation.R
CancerSubtypes/R/data.R
CancerSubtypes/R/featureSelection.R
CancerSubtypes/R/internal.R
CancerSubtypes/README.md
CancerSubtypes/build
CancerSubtypes/build/vignette.rds
CancerSubtypes/data
CancerSubtypes/data/GeneExp.rda
CancerSubtypes/data/miRNAExp.rda
CancerSubtypes/data/status.rda
CancerSubtypes/data/time.rda
CancerSubtypes/inst
CancerSubtypes/inst/NEWS
CancerSubtypes/inst/doc
CancerSubtypes/inst/doc/CancerSubtypes-vignette.R
CancerSubtypes/inst/doc/CancerSubtypes-vignette.Rmd
CancerSubtypes/inst/doc/CancerSubtypes-vignette.html
CancerSubtypes/inst/unitTests
CancerSubtypes/inst/unitTests/test_FSbyCox.R
CancerSubtypes/man
CancerSubtypes/man/DiffExp.limma.Rd
CancerSubtypes/man/ExecuteCC.Rd
CancerSubtypes/man/ExecuteCNMF.Rd
CancerSubtypes/man/ExecuteSNF.CC.Rd
CancerSubtypes/man/ExecuteSNF.Rd
CancerSubtypes/man/ExecuteiCluster.Rd
CancerSubtypes/man/FSbyCox.Rd
CancerSubtypes/man/FSbyMAD.Rd
CancerSubtypes/man/FSbyPCA.Rd
CancerSubtypes/man/FSbyVar.Rd
CancerSubtypes/man/GeneExp.Rd
CancerSubtypes/man/data.checkDistribution.Rd
CancerSubtypes/man/data.imputation.Rd
CancerSubtypes/man/data.normalization.Rd
CancerSubtypes/man/drawHeatmap.Rd
CancerSubtypes/man/miRNAExp.Rd
CancerSubtypes/man/saveFigure.Rd
CancerSubtypes/man/sigclustTest.Rd
CancerSubtypes/man/silhouette_SimilarityMatrix.Rd
CancerSubtypes/man/spectralAlg.Rd
CancerSubtypes/man/status.Rd
CancerSubtypes/man/survAnalysis.Rd
CancerSubtypes/man/time.Rd
CancerSubtypes/tests
CancerSubtypes/tests/runTests.R
CancerSubtypes/vignettes
CancerSubtypes/vignettes/CancerSubtypes-vignette.Rmd