Normally you do a first analysis for miRNA annotation and so on ourside R, and then use R and bioconductor packages for differential expression or donwstream analysis.
It's possible you can do all with R, but we use: https://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html#smallrna-seq
For sure you need to spend some time how to use the tools, so nothing that will be running in 5 min. You will see the main steps and outputs you can have with small RNAseq data.
This also depends very much on which species you are working on. But check out this recently published online collection of tools. Seems like you can pretty much do the entire pipeline here: http://bioinfo5.ugr.es/srnatoolbox/srnabench/