SOFTWARE

CMARRT
 

DESCRIPTION

An R package for the analysis of tiling array data that incorporates the correlation structures among probe measurements.

DOWNLOADS

Package source : CMARRT_1.3.tar.gz
Windows binary : CMARRT_1.3.zip
Vignette : pdf

REFERENCE

Kuan, P., Chun, H., and Keles, S. (2008). CMARRT: A tool for the analysis of ChIP-Chip data from tiling arrays by incorporating the correlation structure. Pac Symposium of Biocomputing, 515-526.
[PubMed] [Article Link]

 

LumiWCluster
 

DESCRIPTION

An R package that implements a weighted model based clustering for Illumina BeadArray Methylation Assays.

DOWNLOADS

Package source : LumiWCluster_1.0.tar.gz
Windows binary : LumiWCluster_1.0.zip
Vignette : pdf

REREFENCE

Kuan, P., Wang, S., Zhou, X., and Chu, H. (2010). A statistical framework for Illumina DNA methylation arrays. Bioinformatics, 26 (22): 2849-2855.
[PubMed] [Article Link]

 

mosaics
 

DESCRIPTION

An R package for the analysis of one-sample or two-sample ChIP-seq data.

DOWNLOADS

Package source : mosaics_1.0.0.tar.gz
Windows binary : mosaics_1.0.0.zip
MacOS 10.5 (Leopard) binary: mosaics_1.0.0.tgz
Vignette : pdf]

REFERENCE

Kuan, P., Chung, D., Pan, G., Thomson, J., Stewart, R., and Keles, S. (2011). A Statistical Framework for the Analysis of ChIP-Seq Data. Journal of the American Statistical Association, doi:10.1198/jasa.2011.ap09706.
[PubMed] [Article Link]

 

NHMMfdr
 

DESCRIPTION

An R package that implements the non-homogeneous Hidden Markov Model based FDR control for multiple comparison adjustment under dependence.

DOWNLOADS

Package source : NHMMfdr_1.0.1.tar.gz]
Vignette : pdf]

REFERENCE

Kuan, P., and Chiang, D. (2012). Integrating Prior Knowledge in Multiple Testing under Dependence with Applications to Detecting Differential DNA Methylation. Biometrics, 68 (3): 774-783.
[PubMed] [Article Link]

 

predictSGRNA
 

DESCRIPTION

An R package that predicts sgRNA efficiency.

DOWNLOADS

Package source : predictSGRNA_1.0.1.tar.gz
Vignette : pdf
Sample Data : SampleData.txt

REFERENCE

Kuan, P., Powers, S., He, S., Li, K., Zhao, X., Huang, B. (2017). A systematic evaluation of nucleotide properties for CRISPR sgRNA design. BMC Bioinformatics, 18: 297.
[PubMed] [Article Link]

 

methylDMV
 

DESCRIPTION

An R package that performs simultaneous detection of differential methylation and variability with confounder adjustment.

DOWNLOADS

Package source : methylDMV_1.0.tar.gz
Vignette : pdf

REFERENCE

Kuan, P., Song, J., He, S. (2017). methyldmv: Simultaneous detection of differential DNA methylation and variability with confounder adjustment. Pacific Symposium of Biocomputing, 22: 461-472.
[PubMed] [Article Link]

 

methylGSA
 

DESCRIPTION

An Bioconductor package that performs gene set enrichment analysis with length bias adjustment in DNA methylation data.

DOWNLOADS

Package source : Click here for the Bioconductor link
Bioconductor Vignette/Demo: HTML
Shiny App : Click here for instruction
Shiny App Vignette/Demo: HTML

REFERENCE

Ren, X., Kuan, P. (2019). methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics. 35 (11): 1958-1959
[PubMed] [Article Link]

 

JumpTest
 

DESCRIPTION

An R package that performs a fast simulation on stochastic volatility model with jump tests, p-values pooling and FDR adjustments.

DOWNLOADS

Package source : Click here for the CRAN link
Vignette: HTML

REFERENCE

Li, K., He, K., Nie, L., Zhu, W., Kuan, P. (2019) Nonparametric Tests for Jump Detection via False Discovery Rate Control: A Monte Carlo Study. Journal of Risk Model Validation. 13 (3): 23-44
[Article Link]

 

NBAMSeq
 

DESCRIPTION

An Bioconductor package based on the generalized additive model for detecting non-linear association with phenotypes in RNA-Seq data.

DOWNLOADS

Package source : Click here for the Bioconductor link
Bioconductor Vignette/Demo: HTML

REFERENCE

Ren, X., Kuan, P. (2019). Negative Binomial Additive Model for RNA-Seq Data Analysis. BMC Bioinformatics. (21): 1-15
[PubMed] [Article Link]

 

glmaag
 

DESCRIPTION

An R package that implements adaptive LASSO and network regularized generalized linear models.

DOWNLOADS

Package source : Click here for the CRAN link
Vignette: HTML

REFERENCE

Li, K., Wang, X., Kuan, P. (2019).Mixture Network Regularized Generalized Linear Model with Feature Selection. bioRxiv, 678029.
[Article Link]

 

RNAAgeCalc
 

DESCRIPTION

A multi-tissue transcriptional age calculator.

DOWNLOADS

Bioconductor Package : Click here for instruction and download
Vignette/Demo: HTML
ShinyApp : Click here for instruction and download
Shiny App Vignette/Demo: HTML
Python Package : Click here for instruction and download
Python Tutorial: HTML

REFERENCE

Ren, X., Kuan, P. (2020). RNAAgeCalc: A multi-tissue transcriptional age calculator. PLOS One. 15 (8): e0237006
[PubMed] [Article Link]