Rail-RNA: scalable analysis of RNA-seq splicing and coverage. - Abhinav Nellore; Leonardo Collado-Torres; Andrew E. Jaffe; José Alquicira-Hernández; Christopher Wilks; Jacob Pritt; James Morton; Jeffrey T. Leek; Ben Langmead (Bioinform., 2017)

Programmatic access to bacterial regulatory networks with regutools. - Joselyn Chávez; Carmina Barberena-Jonas; Jesus E. Sotelo-Fonseca; José Alquicira-Hernández; Heladia Salgado; Leonardo Collado-Torres; Alejandro Reyes (Bioinform., 2020)

Nebulosa recovers single-cell gene expression signals by kernel density estimation. - José Alquicira-Hernández; Joseph E. Powell (Bioinform., 2021)