Software

chunglab.io

• The portal for the software and web interface developed by Chung lab.

Spatial Transcriptomics Data Analysis:

SPRUCE: Tissue architecture identification using spatial transcriptomics data.

• CRAN

• GitHub page

MAPLE: Multi-sample analysis, including differential analysis, based on spatial transcriptomics data.

• CRAN

• GitHub page

BANYAN: Analysis of community connectivity using spatial transcriptomics data.

• GitHub page

Statistical Genetics:

GGPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture.

• Bioconductor (Release)

• GitHub page

GGPA 2.0: A graphical model for multi-disease genetic analysis and integration of functional annotation data.

• GitHub page

GPA-Tree: Genetic analysis by integrating functional annotation data using a decision tree algorithm.

• GitHub page

GPA: Genetic analysis incorporating Pleiotropy and Annotation.

• Bioconductor (Release)

• GitHub page

Biomedical Literature Mining:

GAIL: Web interface to investigate gene-gene association based on the biomedical literature mining.

• GAIL web interface

DDNet: Web interface to investigate disease-disease network based on the biomedical literature mining.

• DDNet web interface

LitSelect: Web interface to download the biomedical literature mining data for the PALMER analysis.

• LitSelect web interface

PALMER: A constrained biclustering algorithm to improve pathway annotation based on the biomedical literature mining.

• GitHub page

bayesGO: A statistical framework for biomedical literature mining.

• GitHub page

Visualization:

ShinyGPA: An interactive and flexible visualization framework to investigate the pleiotropic architecture.

• GitHub page

hubViz: Hub-centric Visualization.

• GitHub page

ChIP-seq Data Analysis:

MOSAiCS: MOdel-based one and two Sample Analysis and Inference for ChIP-Seq data.

• Bioconductor (Release) (BiocViews: mosaics, mosaicsExample)

• mosaics package in ENCODE software page

• MOSAiCS FTP server: provides M, GC, and N files for various genomes such as HG19, MM9, and MM10.

• mosaics software Google group

• GitHub page

dPeak: High Resolution TFBS Identification using ChIP-exo, PET and SET ChIP-Seq data.

• Bioconductor (Release)

• GitHub page

CSEM: Multi-read allocation of ChIP-Seq data.

• Software page

High Dimensional Data Analysis:

SPLS: Sparse Partial Least Squares (SPLS) Regression and Classification.

• Software page

• CRAN

InGRiD: Integrative Genomics Robust iDentification of cancer subgroups.

• GitHub page