lncDIFF is now avaialbe on CRAN at https://cran.r-project.org/web/packages/lncDIFF/index.html
This is a tool for low-counts long non-coding RNA (lncRNA) differential expression analysis, using generalized linear model with zero-inflated exponential quasi likelihood. It can be applied to commonly used normalized counts, e.g. RPKM (FPKM), TMM, UQ. The package
install.packages("lncDIFF")
Li, Qian, et al. "lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA." BMC genomics 20.1 (2019): 539.