MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis. - Seungyeul Yoo; Tao Huang; Joshua D. Campbell; Eunjee Lee; Zhidong Tu; Mark W. Geraci; Charles A. Powell; Eric E. Schadt; Avrum Spira; Jun Zhu (PLoS Comput. Biol., 2014)

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data. - Zhe Wang 028; Junming Hu; W. Evan Johnson; Joshua D. Campbell (BMC Bioinform., 2019)

ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects. - Irzam Sarfraz; Muhammad Asif 002; Joshua D. Campbell (Bioinform., 2021)

Interactive analysis of single-cell data using flexible workflows with SCTK2. - Yichen Wang; Irzam Sarfraz; Nida Pervaiz; Rui Hong; Yusuke Koga; Vidya Akavoor; Xinyun Cao; Salam Alabdullatif; Syed Ali Zaib; Zhe Wang 028; Frederick Jansen; Masanao Yajima; et al. (Patterns, 2023)

Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM. - Nicholas K. O'Neill; Thor D. Stein; Junming Hu; Habbiburr Rehman; Joshua D. Campbell; Masanao Yajima; Xiaoling Zhang; Lindsay A. Farrer (BMC Bioinform., 2023)