Key resources for learning R for basic bioinformatic analyses

R installation: https://cran.r-project.org/

RStudio installation: https://rstudio.com/products/rstudio/download/

Using R for bioinformatics data analysis:

1. An introduction to R: https://cran.r-project.org/doc/manuals/R-intro.pdf

2. The R Book: PDF: https://www.cs.upc.edu/~robert/teaching/estadistica/TheRBook.pdf

3. UC Riverside R Manual: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual

4. Bioconductor: https://www.bioconductor.org/
   

Courses on Bioconductor： https://www.bioconductor.org/help/course-materials/

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

Single cell genomics tools:

1. Seurat https://satijalab.org/seurat/

2. UK Sanger sources: https://scrnaseq-course.cog.sanger.ac.uk/website/introduction-to-single-cell-rna-seq.html

3. Current best practices in single cell analysis: https://www.embopress.org/doi/10.15252/msb.20188746

Other genomics toolkits:

Broad GATK Suite:  https://gatk.broadinstitute.org/hc/en-us