Intermediate data and code for all analyses described in "A new paradigm for leprosy diagnosis based on host gene expression". The files are organized into 4 main directories: Main RNA-seq analysis; Public data reanalysis; Correlation analyses; RNA-seq validation by RT-qPCR. Some files are needed in between these directories. Therefore, all data should be downloaded and decompressed apropriately to allow re-running analyes If you have any inquiries, please get in touch. All code was tested in Linux with R 3.6.1 and with package versions according to what is listed in package_versions.txt.