Tools
We aim to develop statistical and computational software for analyzing large-scale biological and medical data. All of our software, pipeline, datasets are open-source. We believe in reproducibility in science and committed to make our code cleanly written, well-documented and reproducbile.
For a full list of our software/database, please see our Github page.
scTAPASscTAPAS (single-cell Transcriptome Allelic Prediction and Association Studies) is a set of Nextflow pipelines for imputing genotypes (and preparing MHC-region variants for downstream HLA imputation) from donor-wise hg38-aligned single-cell RNA-seq BAM files.
ORBITThe goal of ORBIT is to detect concordant signals across omics study
HLA-TAPASHLA-TAPAS (HLA-Typing At Protein for Association Studies) is an HLA-focused pipeline that can handle HLA reference panel construction (MakeReference), HLA imputation (SNP2HLA), and HLA association (HLAassoc).
covariate-adjusted LD score regressioncov-LDSC is a method to provide robust hg2 estimates from GWAS summary statistics and in-sample LD estimates in admixed populations.