Software
This page includes our open-sourced softwares.
We develop omics software!
a computational method for rapid and accurate profiling of the adaptive immune repertoire from bulk RNA-Seq data
a computational protocol allowing to differentiate PCR duplicates from biological duplicates using UMIs; designed in collaboration with Prof. Kelsey Martin
a computational method to reconstruct the haploid transcriptome of a diploid organism from long single molecule reads
a method to visualize the metagenomics data in the form of interactive coverage plots. It allows to detect false positives based on the coverage corresponding microbial genomes
a method for detecting low abundance viral and fungal organisms in metagenomic sample
a method for comprehensive virome, mycobiome, and eukaryome profiling on the strain level. Needle combines alignment and assembly strategies
a computational protocol to discover the source of all reads, which originate from complex RNA molecules, recombined B and T cell receptors and microbial communities
a computational method for rapid and accurate profiling of the adaptive immune repertoire from bulk RNA-Seq data
a software platform to mine discarded tumor sequences from clinical sequencing
an open-source web application that tracks the progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system
a comprehensive jupyter notebook based platform for T-Cell receptor (TCR) data analysis to facilitate reproducibility and rigor of immunogenomics research.