ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)
Version 1.12.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorYing Shen, Andrea H. Bild, W. Evan Johnson, and Mumtehena Rahman
Bioconductor views Bayesian GeneExpression Pathways Software
Date of publicationNone
MaintainerYing Shen <yshen3@bu.edu>, W. Evan Johnson <wej@bu.edu>, David Jenkins <dfj@bu.edu>, Mumtehena Rahman <moom.rahman@utah.edu>
LicenseMIT + file LICENSE
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ASSIGN")

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
ComBat.step2: Perform the second step of ComBat
gather_assign_results: Gather the ASSIGN results in a specific directory
geneList1: Pathway signature gene sets
gfrn_geneList: Pathway Signature Gene Lists
merge_drop: Combine two data frames
optimizeGFRN: Optimize GFRN gene lists lengths
pcaplot: Display a PCA Plot of the Data
runassignGFRN: Run optimized single pathway ASSIGN
testData1: Gene expression profiling from cancer patients (test dataset)
trainingData1: Gene expression profiling from cell line preturbation...

Functions

ComBat.step2 Man page Source code
assign.convergence Man page Source code
assign.cv.output Man page Source code
assign.mcmc Man page Source code
assign.output Man page Source code
assign.preprocess Man page Source code
assign.summary Man page Source code
assign.wrapper Man page Source code
bayes.gene.selection Source code
box.plot.test Source code
data_prep_s1 Source code
data_prep_s2 Source code
gather_assign_results Man page Source code
geneList1 Man page
geneMatch_sub2 Source code
gfrn_geneList Man page
heatmap.test.pos Source code
heatmap.test.prior Source code
heatmap.train Source code
merge_drop Man page Source code
optimizeGFRN Man page Source code
pcaplot Man page Source code
qc Source code
runassignGFRN Man page Source code
scatter.plot.test Source code
scatter.plot.train Source code
testData1 Man page
trainingData1 Man page

Files

.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R
R/ASSIGN-package.R
R/ComBat.step2.R
R/assign.covergence.R
R/assign.cv.output.R
R/assign.mcmc.R
R/assign.output.R
R/assign.preprocess.R
R/assign.summary.R
R/assign.wrapper.R
R/bayes.gene.selection.R
R/box.plot.test.R
R/data_prep_s1.R
R/data_prep_s2.R
R/geneMatch_sub2.R
R/heatmap.test.pos.R
R/heatmap.test.prior.R
R/heatmap.train.R
R/misc_functions.R
R/optimizeGFRN.R
R/qc.R
R/runassignGFRN.R
R/scatter.plot.test.R
R/scatter.plot.train.R
README.md
build
build/vignette.rds
data
data/datalist
data/geneList1.rda
data/gfrn_geneList.rda
data/testData1.rda
data/trainingData1.rda
inst
inst/doc
inst/doc/ASSIGN.vignette.R
inst/doc/ASSIGN.vignette.Rnw
inst/doc/ASSIGN.vignette.pdf
man
man/ComBat.step2.Rd
man/assign.convergence.Rd
man/assign.cv.output.Rd
man/assign.mcmc.Rd
man/assign.output.Rd
man/assign.preprocess.Rd
man/assign.summary.Rd
man/assign.wrapper.Rd
man/gather_assign_results.Rd
man/geneList1.Rd
man/gfrn_geneList.Rd
man/merge_drop.Rd
man/optimizeGFRN.Rd
man/pcaplot.Rd
man/runassignGFRN.Rd
man/testData1.Rd
man/trainingData1.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_preprocess.R
vignettes
vignettes/ASSIGN.vignette.Rnw
ASSIGN documentation built on May 20, 2017, 9:52 p.m.