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Workshop Preparation

HPC and dataset check

Things to check:

  • Are you able to login into NeSI (If not please get in touch with Dini - dinindu.senanayake@nesi.org.nz)
  • Do you have RStudio installed on your laptop

Once you login to NeSI, you will see a folder RNA_seq in your home directory:

$ cd RNA_seq

$ ls -F
Genome/ Raw/

If you see the RNA_seq directory with 2 sub-directories: Genome/ and Raw/, yayyy you are good to go.

If not, no pressure, we can still copy the RNA_seq directory to your home directory.

$ cp -r /nesi/nobackup/nesi02659/RNA_seq/ /home/Your_Username

$ ls
RNA_seq

Differential expression prep

These are the packages needed for the differential expression analysis

install DESeq2, edgeR, limma, systemPipeR


# Older versions of R (older than 3.5)
> source("https://bioconductor.org/biocLite.R")

> biocLite("DESeq2")

# Newer versions of R
> if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

> BiocManager::install("DESeq2")

# Installing edgeR will also install limma as it is a dependency package
> BiocManager::install("edgeR")

# systemPipeR: R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.

> BiocManager::install("systemPipeR")

Overrepresentation analysis prep

install goseq, ggplot2, org.Sc.sgd.db, venn

# goseq: R package for detecting Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data
> BiocManager::install("goseq")

# ggplot: is a data visualization package
> install.packages("ggplot2")

# org.Sc.sgd.db: Genome wide annotation for Yeast, primarily based on mapping using ORF identifiers from SGD.
> BiocManager::install("org.Sc.sgd.db")

# venn: Draws and displays Venn diagrams up to 7 sets, and any Boolean union of set intersections.

> install.packages("venn")