Softwares

Python/Conda package

• Cellcano: Cellcano is developed to do supervised cell type identification (celltyping) in scATAC-seq data. Cellcano is a two-round algorithm which utilizes confident cells predicted in the first round to predict remaining cells in the second round. PyPI, conda, code

Bioconductor package

• LRcell (Differential cell type change analysis using Logitstic/linear Regression): LRcell is developed to identify specific (sub-)cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment.

Web server

• BARTweb(Binding Analysis for Regulation of Transcription web): A web server hosted for performing BART analysis, which is a bioinformatics tool for predicting functional factors (including transcription factors and chromatin regulators) that bind at cis-regulatory regions to regulate gene expression in human or mouse, taking a query gene list or a ChIP-seq dataset as input.

Research pipleines

• Explorations on strategies of constructing reference dataset for celltyping. Our paper titled “Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction” is accepted on Genome Biology. benchmark code, paper