Introduction to R and Bioconductor for analysing sRNA-Seq data (2021)

This webpage contains introductory practicals about using R and Bioconductor for genomic analyses, geared towards small RNA-Seq data.

Installing R and Bioconductor


1. Learning to use R


2. Learning to use R (part 2)


3. Exploring genome annotation from Ensembl


4. Introduction to Bioconductor with Biostrings


The next two practicals require running commands on the Linux terminal. You might need to spend some time on Unix/Linux tutorials such as:
• UNIX Tutorial for Beginners
• The Unix Shell (The Carpentries)



5. Linux: Processing raw sequencing fastq files


6. Linux: Mapping sRNA-Seq sequences with bowtie



7. Genome annotation and SAM/BAM alignments


8. Differential expression analysis for small RNA-Seq


9. Discovering enriched sequence motifs


10. Extra R/BioC stuff

Some useful links

R & Bioconductor

• Main R website


• RStudio


• Bioconductor
  • Installing Bioconductor
  
  Briefly: First install the latest R version on your computer. Then start R, and copy/paste the following instructions.
  From version 3.5 onwards:
  

  install.packages("BiocManager")
  BiocManager::install()