Software

Software (Github)

eQTL Analysis

• MT-eQTL: an empirical Bayesian approach for multi-tissue eQTL analysis (Paper, Matlab code, R code*) *credit to Andrey A. Shabalin

• HT-eQTL: a scalable extension of MT-eQTL to a large number of tissues (Paper, Matlab code) 

• QRank: a quantile regression approach for eQTL detection (Paper, R package*) *credit to Xiaoyu Song

Dimension Reduction

• SuperPCA: a comprehensive R Package* (*credit to Jiayi Ji and Haocheng Ding) for supervised principal component analysis, subsuming SupSVD, SupSFPC, SIFA and SupCP 

• SupSVD: a supervised singular value decomposition method (Paper, Matlab code)

• SupSFPC: a supervised sparse and functional principal component analysis method (Paper, Matlab code)

• SIFA: a supervised integrative factor analysis method for multi-view data (Paper, Matlab code)

• SupCP: a supervised CP factorization method for tensor array data (Paper, Matlab code*) *credit to Eric F. Lock

• SLIDE: an integrative decomposition method for multi-view data (Paper, R code*) *credit to Irina Gaynanova

• EFPCA: an exponential family functional principal component analysis method (Paper, Matlab code)

• GIPCA: an integrative principal component analysis for heterogeneous data with blockwise missing structure (Paper, R code*) *credit to Huichen Zhu

• ZIPFA: an zero-inflated Poisson factor analysis model for microbiome data (Paper, R/Matlab code*) *credit to Tianchen Xu

• PAA: principal amalgamation analysis for compositional data (Paper, R code*) *credit to Yan Li

Regression and Association Analysis 

• GAS: a generalized association analysis method (Paper, Matlab code)

• iRRR: a multivariate regression method bridging group-lasso and low-rank models (Paper, Matlab code)

• mRRR: a reduced-rank multivariate regression method with mixed-type responses (Paper, R package*) *credit to Kun Chen

• Compack: regression with compositional covariates (Paper, Package*) *credit to Zhe Sun

• RelativeShift: regularized regression framework for compositional data (Paper, Matlab code)

• ECLasso: fast algorithm for lasso with equality constraints (Paper, code*) *credit to Lam Tran

• CAMP: censoring-based differential relative abundance analysis (Paper, code*) *credit to Lap Sum Chan

• TRIO: scalar-on-tensor regression with incomplete observations (Paper, Matlab code*) *credit to Tianchen Xu

Others

• CORALS: a generalized coclustering method for tensor data with various data types (Paper, Matlab code)

• tF-Hazard: a two-way functional method for estimating hazards function with dual timescales (Paper, Matlab code)

• VCERGM: a varying-coefficient ERGM method for modeling temporal networks (Paper, R code*) *credit to Jihui Lee