Chi Wang

bacr

bacr is an R package that implements the Bayesian Adjustment for Confounding (BAC) method for estimating the average causal effect of a treatment on an outcome from cohort studies. The software package is available at CRAN.

References

  1. Wang C, Parmigiani G, Dominici F and Zigler CM. Accounting for Uncertainty in Confounder and Effect Modifier Selection when Estimating Average Causal Effects in Generalized Linear Models. Biometrics, 71(3):654-65, 2015.
  2. Wang C, Parmigiani G and Dominici F. Bayesian Effect Estimation Accounting for Adjustment Uncertainty (with discussion). Biometrics, 68(3):661-71, 2012.

NanoStringDiff

NanoStringDiff is an R package to perform differential expression analysis based on gene expression data generated from the NanoString nCounter system. The software package is available at Bioconductor.

Reference

  1. Wang H, Horbinski C, Wu H, Liu Y, Sheng S, Liu J, Weiss H, Stromberg A, Wang C. NanoStringDiff: A Novel Statistical Method for Differential Expression Analysis Based on NanoString nCounter Data. Nucleic Acids Research, 44(20): e151, 2016.

SDAMS

SDAMS is an R package that implements a semiparametric method for differential abundance analysis of proteomic and metabolomic data. The software package is available at Bioconductor.

Reference

  1. Li Y, Fan TWM, Lane AN, Kang WK, Arnold SM, Stromberg AJ, Wang C*, Chen Li*. SDA: A semi-parametric differential abundance analysis method for metabolomics and proteomics data. BMC Bioinformatics, 20(1):501, 2019. * Co-corresponding authors

PATOPA

PATOPA is a bioinformatics software to delineate the temporal order of driver mutations during carcinogenesis by leveraging functional annotation and pathway information. The software is available at GitHub.

Reference

  1. Wang M, Yu T, Liu J, Chen L, Stromberg AJ, Villano JL, Arnold SM, Liu C, Wang C. A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis. BMC bioinformatics, 20:620, 2019.

DASEV

DASEV is an R package that implements a two-part model with Bayesian shrinkage estimation of variance for differential abundance analysis of proteomic and metabolomic data. The software package is available here.

Reference

  1. Huang Z, Lane AN, Fan TW, Higashi RM, Weiss HL, Yin X, Wang C. Differential Abundance Analysis with Bayes Shrinkage Estimation of Variance (DASEV) for Zero-Inflated Proteomic and Metabolomic Data. Scientific Reports, 10(1):876, 2020.

MEScan

MEScan is a bioinformatics software to identify cancer driver mutations by genome-wide screen of mutually exclusive mutation patterns. The software is available at GitHub.

Reference

  1. Liu S, Liu J, Xie Y, Zhai T, Hinderer EW, Stromberg AJ, Canderford NL, Kolesar JM, Moseley HNB, Chen L, Liu C, Wang C. MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations. Bioinformatics, btaa957, 2020.