Package: ASSIGN 1.49.0

Ying Shen

ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

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 literature 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.

Authors:Ying Shen, Andrea H. Bild, W. Evan Johnson, and Mumtehena Rahman

ASSIGN_1.49.0.tar.gz
ASSIGN_1.49.0.zip(r-4.7)ASSIGN_1.49.0.zip(r-4.6)ASSIGN_1.49.0.zip(r-4.5)
ASSIGN_1.49.0.tgz(r-4.6-any)ASSIGN_1.49.0.tgz(r-4.5-any)
ASSIGN_1.49.0.tar.gz(r-4.7-any)ASSIGN_1.49.0.tar.gz(r-4.6-any)
ASSIGN_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ASSIGN/json (API)
NEWS

# Install 'ASSIGN' in R:

install.packages('ASSIGN', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/compbiomed/assign/issues

Datasets:

excludegenes - Exclude Gene List
geneList1 - Pathway signature gene sets
gfrn_geneList - Pathway Signature Gene Lists
testData1 - Gene expression profiling from cancer patients
trainingData1 - Gene expression profiling from cell line perturbation experiments

On BioConductor:ASSIGN-1.49.0(bioc 3.24)ASSIGN-1.48.0(bioc 3.23)

software geneexpression pathways bayesian

7.38 score 2 stars 1 packages 66 scripts 480 downloads 54 mentions 13 exports 83 dependencies

Last updated from:a0d4832531. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	165
linux-devel-x86_64	NOTE	182
source / vignettes	OK	231
linux-release-x86_64	NOTE	212
macos-release-arm64	NOTE	89
macos-oldrel-arm64	NOTE	88
windows-devel	NOTE	100
windows-release	NOTE	118
windows-oldrel	NOTE	105
wasm-release	OK	117

Exports:assign.convergence assign.cv.output assign.mcmc assign.output assign.preprocess assign.summary assign.wrapper ComBat.step2 gather_assign_results merge_drop optimizeGFRN pcaplot runassignGFRN

Dependencies:annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob cachem caTools cli codetools cpp11 crayon curl DBI edgeR expm farver fastmap formatR futile.logger futile.options genefilter generics ggplot2 glue gplots gtable gtools httr IRanges isoband jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime msm mvtnorm nlme openssl pillar pkgconfig png R6 RColorBrewer Rlab rlang RSQLite S4Vectors S7 scales Seqinfo snow statmod survival sva sys tibble utf8 vctrs viridisLite withr XML xtable XVector yaml

Introduction to the ASSIGN Package

Ying Shen, David Jenkins, W. Evan Johnson

Rendered fromASSIGN.vignette.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2018-10-27
Started: 2018-01-23

Help page	Topics
Check the convergence of the MCMC chain	assign.convergence
Cross validation output	assign.cv.output
The Gibbs sampling algorithm to approximate the joint distribution of the model parameters	assign.mcmc
Prediction/validation output for test data	assign.output
Input data preprocessing	assign.preprocess
Summary of the model parameters estimated by the Gibbs sampling algorithm	assign.summary
ASSIGN All-in-one function	assign.wrapper
Perform the second step of ComBat	ComBat.step2
Exclude Gene List	excludegenes
Gather the ASSIGN results in a specific directory	gather_assign_results
Pathway signature gene sets	geneList1
Pathway Signature Gene Lists	gfrn_geneList
Combine two data frames	merge_drop
Optimize GFRN gene lists lengths	optimizeGFRN
Display a PCA Plot of the Data	pcaplot
Run optimized single pathway ASSIGN	runassignGFRN
Gene expression profiling from cancer patients (test dataset)	testData1
Gene expression profiling from cell line perturbation experiments (training dataset)	trainingData1

Package: ASSIGN 1.49.0

ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

Introduction to the ASSIGN Package

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)