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
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
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]
methylDeConv
DESCRIPTION
A Computational Deconvolution Pipeline for Methylation Data.
DOWNLOADS
Github :
Click here for instruction and download
REFERENCE
Song, J., Kuan, P.
(2022). A systematic assessment of cell type deconvolution
algorithms for DNA methylation data. To appear in
Briefings in Bioinformatics.
[PubMed] [Article Link]