(a selection)
- AnnoGen: A python toolkit for annotation of three pragmatic genomic features of the GRCh38 genome - Quanhu "Tiger" Sheng, Hui Yu, Olufunmilola Oyebamiji, Jiandong Wang, Danqian Chen, Scott Ness, Ying-Yong Zhao, and Yan Guo
- Biostat toolbox Excel add-in - Will Gray
- Cancer-Immu: An immunotherapy-related genomics portal for pan-cancer studies - Jing Yang, Qi Liu, and Yu Shyr
- Characteristics of 3+3 designs in phase I clinical trials - Tatsuki Koyama
- CPDSeqer: A python package for CPD sequence data analysis - Quanhu "Tiger" Sheng, Hui Yu, Mingrui Duan, Scott Ness, Jiapeng He, Huining Kang, Limin Jiang, John Wyrick, Peng Mao, and Yan Guo
- Domain Damage Index: For prioritizing the pathogenicity of missense variants - Hua-Chang Chen, Jing Wang, Qi Liu, and Yu Shyr
- EVPSort: Extracellular Vesicle and Particle profiling and sorting - Hua-Chang Chen, Jing Wang, Robert Coffey, James Patton, Alissa Weaver, Yu Shyr, and Qi Liu
- ExonDel: Detects exon deletions in DNA-seq data - Yan Guo, Shilin Zhao, Quanhu "Tiger" Sheng, and Yu Shyr
- GLMVC: Somatic mutation calling using both DNA and RNAseq data - Quanhu "Tiger" Sheng, Shilin Zhao, Chung-I Li, Yu Shyr, and Yan Guo
- HACER: Human active enhancers database to interpret regulatory variants - Jing Wang, Xizhen Dai, Lynne Berry, Joy Cogan, Qi Liu, and Yu Shyr
- heatmap3: An improved heatmap package - Shilin Zhao, Yan Guo, Quanhu "Tiger" Sheng, and Yu Shyr
- Immu-Mela: A multidimensional immuno-genomic portal - Jing Yang, Shilin Zhao, Jing Wang, Quanhu "Tiger" Sheng, Qi Liu, and Yu Shyr
- Mass spectrometry binning software PSB - Huiming Li, Shuo Chen, Don Hong, Ming Li, and Yu Shyr
- Mass spectrometry preprocessing software waveSpec 0.9 - Shuo Chen, Don Hong, and Yu Shyr
- mirSTP: Predicts TSS for human intergenic miRNA using GRO/PRO-seq data - Qi Liu, Jing Wang, Yue Zhao, Chung-I Li, Kristy R. Stengel, Pankaj Acharya, Gretchen Johnston, Scott W. Hiebert, and Yu Shyr
- MultiRankSeq: A multiperspective approach for differential detection in RNA-seq data - Yan Guo, Shilin Zhao, Fei Ye, Quanhu "Tiger" Sheng, and Yu Shyr
- NGSPERL: A semi-automated framework for large scale next generation sequencing data analysis - Quanhu "Tiger" Sheng, Shilin Zhao, Mingsheng Guo, and Yu Shyr
- NRSA: Nascent RNA sequencing analysis - Jing Wang, Yue Zhao, Scott W. Hiebert, Qi Liu, and Yu Shyr
- Optimal selection of adaptive designs in Phase I oncology clinical trials - Sheau-Chiann Chen and Yu Shyr
- Phase I two-stage mTPI design - Sheau-Chiann Chen and Yu Shyr
- Power and sample size estimation software - William Dupont and Dale Plummer
- QC3: A quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling - Yan Guo, Shilin Zhao, Quanhu "Tiger" Sheng, Fei Ye, and Yu Shyr
- Risk score patient survival - Mike Guo and Yu Shyr
- RNA-seq sample size estimation by real data - Shilin Zhao, Chung-I Li, Yan Guo, Quanhu "Tiger" Sheng, and Yu Shyr
- RNA-seq sample size estimation by GLM - Chung-I Li and Yu Shyr
- Script of CSDA for mass spectrometry preprocessing - Shuo Chen
- scPS - tool for calculating power and sample sizes based on generalized estimating equations - Chih-Yuan Hsu, Qi Liu, and Yu Shyr
- scRNABatchQC: Compares multiple sample sets over numerous technological and biological features - Qi Liu, Quanhu "Tiger" Sheng, Marisol Adelina Ramirez, Ken S. Lau, Robert J. Coffey, and Yu Shyr
- scMRMA: Multi-resolution cell type annotation for single cell transcriptomics data - Jia Li, Quanhu "Tiger" Sheng, Qi Liu, and Yu Shyr
- scUniFrac: Quantifies cellular composition diversity across single cell transcriptomics data - Qi Liu, Charles A. Herring, Quanhu "Tiger" Sheng, Jie Ping, Alan J. Simmons, Bob Chen, Amrita Banerjee, Wei Li, Guoqiang Gu, Robert J. Coffey, Yu Shyr, and Ken S. Lau
- TIGER: Tools for intensive genome alignment of extracellular small RNA - Ryan M. Allen, Shilin Zhao, Marisol A. Ramirez Solano, Wanying Zhu, Danielle L. Michell, Yuhuan Wang, Yu Shyr, Praveen Sethupathy, MacRae F. Linton, Gregory A. Graf, Quanhu "Tiger" Sheng, and Kasey C. Vickers
- Two-stage Phase II oncology clinical trials designs - Fei Ye and Yu Shyr
- Weighted flexible compound covariate method - Yu Shyr and development team