GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. - Umadevi Paila; Brad A. Chapman; Rory D. Kirchner; Aaron R. Quinlan (PLoS Comput. Biol., 2013)

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test. - Emmanuel Dimont; Jiantao Shi; Rory D. Kirchner; Winston Hide (Bioinform., 2015)

bcbioRNASeq: R package for bcbio RNA-seq analysis. - Michael J. Steinbaugh; Lorena Pantano; Rory D. Kirchner; Víctor Barrera; Brad A. Chapman; Mary E. Piper; Meeta Mistry; Radhika S. Khetani; Kayleigh Rutherford; Oliver Hofmann 001; John N. Hutchinson; Shannan J. Ho Sui (F1000Research, 2017)