Pretty much all Bioconductor courses and workflows are excellent resources for doing bioinformatics analysis with R!

https://www.bioconductor.org/help/course-materials/

https://www.bioconductor.org/help/workflows/

Enjoy

Coursera has some pretty good introductory courses to R with real life problems and everything!

If you're asking in general for introduction into bioinformatics, there is a lot of literature out there. Specifically for R, there is no particular literature encompassing all the tools used for NGS data analysis (at least not that I know of). You need to know specifically what are you looking for, and then find information about particular tool. E.g. I usually use Phyloseq package for 16S data analysis (https://joey711.github.io/phyloseq/index.html), while for metagenomics and multivariate statistics I've become fond of MixOmics package (http://mixomics.org/).

I took a basic R class on coursera which taught me the basics. One tool I have found quite usefull in single cell genomics is Seurat:

http://satijalab.org/seurat/

Pretty much all Bioconductor courses and workflows are excellent resources for doing bioinformatics analysis with R!

https://www.bioconductor.org/help/course-materials/

https://www.bioconductor.org/help/workflows/

Enjoy

Recommed edx course by Rafael Irrizary.

This is a series course and will introduce you to bioinformatics analysis. It basicly use R and bioconductor. But it covers a lot more, including methylation and ChIP-seq analysis.

If you only want to learn R, you can found tons of videos even on Youtube. So don't worry about that and just follow any series video.

The most important thing is to get hands-on. So I suggest you can start with TCGA or GEO data to try run your R code.

By the way F1000 research is a good place to find pipelines and very detailed tutorial of bioconductor package in real dataset.,

Hope it helps.

Many of these answers are great ways of identifying packages for bioinformatic analysis and getting information about how to use them. I think one of the major hurdles in using many packages is being able to get your data in the right format for the tool. There is a great online book available to learn basic data wrangling and visualization in R here: http://r4ds.had.co.nz/. It's written by Garret Grolemund and Hadley Wickham, and teaches you about dplyr, ggplot, and other aspects of the tidyverse which can be extremely helpful.

I found Kasper Hansen's course on Bioconductor to be very informative. And all of the YouTube videos and R markdown documents are available on his site: http://kasperdanielhansen.github.io/genbioconductor/

http://tryr.codeschool.com/

This online course on Coursera :

https://www.coursera.org/learn/bioconductor

About this course: Learn to use tools from the Bioconductor project to perform analysis of genomic data. This is the fifth course in the Genomic Big Data Specialization from Johns Hopkins University.

Good Luck