Here a few recent reviews of tools for various aspects of RNAseq analysis
van Dam, S., Võsa, U., van der Graaf, A., Franke, L., & de Magalhães, J. P. (2017). Gene co-expression analysis for functional classification and gene–disease predictions. Briefings in Bioinformatics, bbw139–18.
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., et al. (2016). A survey of best practices for RNA-seq data analysis. Genome Biology, 17(1), 1–19.
Castel, S. E., Levy-Moonshine, A., Mohammadi, P., Banks, E., & Lappalainen, T. (2015). Tools and best practices for data processing in allelic expression analysis. Genome Biology, 16(1), 1–12