A list of bioinformatics tools we developed

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tdfdr

• Two-dimensional false discovery rate control for powerful confounder adjustment in omics association studies
• Paper

STA

• Semi-supervised topological analysis (STA), to explore the visualization of data based on Mapper, a topological data analysis method.
• Paper

DVboost

• Adaptive variant filtering using generalized boosted regression models

FFPEinput

• FFPEinput aims to provide RNA input recommendations (RNA concentration and library concentration) for FFPE samples in order to generate adequate data for RNA-seq.
• Paper

scRNAseq-vis

• Web application for analyzing single cell as well as general bulk RNA-seq datasets
• Currently deployed at here

MBDDiff

• MBDDiff is designed specifically for processing MBDCap-seq datasets. MBDDiff contains three modules: quality assessment of datasets and quantification of DNA methylation; determination of differential methylation of promoter regions; and visualization functionalities.
• Paper

XBSeq

• XBSeq is a novel algorithm for testing RNA-seq differential expression (DE), where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises.
• Paper

For a list of all my publications & abstracts, you can view my google scholar profile here