ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

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ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.

Author
Ying Shen, Andrea H. Bild, and W. Evan Johnson
Date of publication
None
Maintainer
Ying Shen <yshen3@bu.edu>
License
MIT
Version
1.10.0

View on Bioconductor

Man pages

assign.convergence
Check the convergence of the MCMC chain
assign.cv.output
Cross validation output
assign.mcmc
The Gibbs sampling algorithm to approximate the joint...
assign.output
Prediction/validation output for test data
assign.preprocess
Input data preprocessing
assign.summary
Summary of the model parameters estimated by the Gibbs...
assign.wrapper
ASSIGN All-in-one function
geneList1
Pathway signature gene sets
testData1
Gene expression profiling from cancer patients (test dataset)
trainingData1
Gene expression profiling from cell line preturbation...

Files in this package

ASSIGN/DESCRIPTION
ASSIGN/NAMESPACE
ASSIGN/R
ASSIGN/R/assign.covergence.R
ASSIGN/R/assign.cv.output.R
ASSIGN/R/assign.mcmc.R
ASSIGN/R/assign.output.R
ASSIGN/R/assign.preprocess.R
ASSIGN/R/assign.summary.R
ASSIGN/R/assign.wrapper.R
ASSIGN/R/bayes.gene.selection.R
ASSIGN/R/box.plot.test.R
ASSIGN/R/data_prep_s1.R
ASSIGN/R/data_prep_s2.R
ASSIGN/R/geneMatch_sub2.R
ASSIGN/R/heatmap.test.pos.R
ASSIGN/R/heatmap.test.prior.R
ASSIGN/R/heatmap.train.R
ASSIGN/R/qc.R
ASSIGN/R/scatter.plot.test.R
ASSIGN/R/scatter.plot.train.R
ASSIGN/build
ASSIGN/build/vignette.rds
ASSIGN/data
ASSIGN/data/datalist
ASSIGN/data/geneList1.rda
ASSIGN/data/testData1.rda
ASSIGN/data/trainingData1.rda
ASSIGN/inst
ASSIGN/inst/doc
ASSIGN/inst/doc/ASSIGN.vignette.R
ASSIGN/inst/doc/ASSIGN.vignette.Rnw
ASSIGN/inst/doc/ASSIGN.vignette.pdf
ASSIGN/man
ASSIGN/man/assign.convergence.Rd
ASSIGN/man/assign.cv.output.Rd
ASSIGN/man/assign.mcmc.Rd
ASSIGN/man/assign.output.Rd
ASSIGN/man/assign.preprocess.Rd
ASSIGN/man/assign.summary.Rd
ASSIGN/man/assign.wrapper.Rd
ASSIGN/man/geneList1.Rd
ASSIGN/man/testData1.Rd
ASSIGN/man/trainingData1.Rd
ASSIGN/vignettes
ASSIGN/vignettes/ASSIGN.vignette.Rnw