Softwares

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.

 

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 array. Bioinformatics, 26 (22): 2849-2855.

 

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.

 

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.Y., (2012). Integrating Prior Knowledge in Multiple
Testing Under Dependence with Applications in Detecting Differential DNA
Methylation. Biometrics, 68 (3): 774-783.

 

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., and Huang, B. (2017). A systematic evaluation
of nucleotide properties for CRISPR sgRNA design. Technical Report.

 

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. and He. S (2016). methylDMV: Simultaneous detection of
differential methylation and variability with confounder adjustment.
Technical Report.