Featured Software

Below is the list of software developed in Li Lab

Cumulus featured image
WDL

Cumulus

Cumulus is a series of open-source cloud-based single-cell genomics data analysis workflows written in WDL language. They use Cloud Computing to achieve scalability on large-scale …

Python

Pegasus

Pegasus is a tool for analyzing transcriptomes of millions of single cells. It is a command line tool, a python package and a base for Cloud-based analysis workflows.

Python

Harmony-Pytorch

Harmony-PyTorch is an efficient PyTorch implementation of Harmony algorithm, used for data integration and batch correction. It has been adopted by rapids-singlecell (a …

Visualizer

Cirrocumulus

Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data, with the following features: Visualize datasets in h5ad, 10x h5, Xenium, loom, Seurat, …

Python

NMF-Torch

NMF-Torch is a PyTorch implementation on Non-negative Matrix Factorization. It provides both batch and online modes for updating the matrices during computation, and aims for high …

C++

PROBer

PROBer is the first unified probabilistic framework for the analysis of a diverse set of sequencing-based ‘toeprinting’ assays. These assays are used to probe RNA secondary …

C++

DETONATE

DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) is a de novo transcriptome assembly evaluation package, which contains two components, …

C++

CSEM

CSEM (ChIP-Seq multi-read allocation using Expectation-Maximization) is one of the first ChIP-Seq multi-mapping read allocators, which allows multi-reads to be utilized by peak …

C++

RSEM

RSEM (RNA-Seq by Expectation-Maximization) is a widely-used RNA-Seq transcript quantification tool. RSEM papers are cited over 5,300 times. It was served in nationwide consortium …