Software

Software for GWAS:

VIMCO A variational inference for multiple correlated outcomes in genome-wide association studies.(R package). [github]

LPG A four-group probabilistic model to leveraging pleiotropy in GWAS (LPG) (R package). [github]

Software for GWAS summary statistics:

EPS An empirical Bayes approach to integrating pleiotropy and tissue-specific information for prioritizing risk genes. Bioinformatics, 2016 [github]

LLR A latent low-rank approach to colocalizing genetic risk variants in multiple GWAS. Bioinformatics, 2017 [github]

REMI Regression on marginal information (R package) [github] [vignette]

Software for TWAS and MR:

CoMM A collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information. Bioinformatics, 2018. (R package) [github] [vignette]

MR-LDP A Mendelian randomization (MR) accounting for linkage disequilbrium and horizontal pleiotropy.(R package). [github]

MR-Corr2 A Mendelian randomization (MR) accounting for correlated genetic variants and correlated horizontal pleiotropy.(R package). [github]

Software for spatial clustering in spatial transcriptomics：

SC.MEB spatial clustering with hidden Markov random field using empirical Bayes. Applying spatial clustering on low-dimensional embeddings from PCs. https://cran.r-project.org/web/packages/SC.MEB/index.html

DR.SC Joint dimension reduction and clustering analysis for single-cell RNA-seq and spatial transcriptomics data. https://cran.r-project.org/web/packages/DR.SC/index.html

PRECAST probabilistic embedding and clustering with alignment for spatial transcriptomics data integration. https://cran.r-project.org/web/packages/PRECAST/index.html

Software portal for spatial transcriptomics