I am a starting PhD student with basic programming skills in python and rather good data-analytical skills in R. I plan to perform RNA sequencing analysis in the near future. To get a better grasp of my data and as a means to grow in my data-analysis skills, I plan to perform the data-analysis myself. However, I am convinced that I could benefit from following a course on how to analyse RNA sequencing data.

While reading in on this topic, I discovered that there is quite a variety of R packages, python modules and other software and pipelines available to analyse RNA sequencing/transcriptomic data. Given the current lack of practical knowledge on this topic, however, I find it rather difficult to distinguish the main differences and possibly more interesting, advantages/disadvantages of the available tools. Could someone with a good background in this topic possibly elaborate on this questions? (By which I mean that I am not specifically looking for someone to promote one or the other tool, but instead hope to get a brief overview.)