Software
Offset-pseudobulk is a lightweight, efficient count-based analysis method that uses an appropriate offset variable to achieve statistical properties similar to GLMMs while improving speed and stability.
Hanbin Lee, Buhm Han. "Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies." Bioinformatics, 40(8). 2024
Keyword: #pseudobulk, #GLMM
MicroPredic is a method for accurately predicting WGS-comparable species-level abundance data using 16S taxonomic profile data.
Chloe Soohyun Jang, Hakin Kim, Donghyun Kim & Buhm Han. "MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data." Genes Genom, 46:701-712. 2024
Keyword: #microbiome, #16s rRNA, #WGS
PASTRY is a meta-analysis method based on an accurate correlation estimator.
Emma E. Kim, Chloe Soohyun Jang, Hakin Kim and Buhm Han. “PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects." BMC Bioinformatics, 25(24), 2024
Keyword : #GWAS, #meta-analysis
privatePRS is a software tool for polygenic risk scoring, ensuring the privacy issue that each individual can be uniquely identified by genotype data consisting of SNPs.
Hakin Kim, Buhm Han “ PrivatePRS: privacy-protecting polygenic risk score calculation by homomorphic encryption” Under Review.
Keyword : #privacy, #homomorphic, #encryption
fastRNA is a scalable framework for single-cell RNA sequencing (scRNA-seq) analysis.
Hanbin Lee, and Buhm Han. “FastRNA: an efficient solution for PCA of single-cell RNA sequencing data based on a batch-accounting count model.” Am J Hum Genet, in press (2022).
Keyword : #single-cell
MarcoPolo is a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering
Kim, Chanwoo, Hanbin Lee, Juhee Jeong, Keehoon Jung, and Buhm Han. “MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering.” Nucleic Acids Research (2022).
Keyword : #single-cell