Installing Bioconductor packages copy

Follow the directions to install DESeq:

To install these packages, start R (version "4.0") by typing "R" at the command line and enter: You will know you are in R when you see something like this at the command line:

Copy and paste this code into at the R command prompt:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq")

Check the install:

browseVignettes("DESeq")

To install DESeq2:

DESeq2

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")

and check the install.

browseVignettes("DESeq2")

To install edgeR:

edgeR

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("edgeR")

and check it.

browseVignettes("edgeR")

Now, exit "R" to get back to your command line by typing "quit()" without the quotes.

Obtain each of the "helper" scripts

curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r
curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r
curl -O http://data.biostarhandbook.com/rnaseq/code/edger.r

and download some data:

curl -O http://data.biostarhandbook.com/rnaseq/code/counts.txt

Then run the script:

cat counts.txt | deseq1.r > results_deseq1.txt

and check the output.

less results_deseq1.txt

See something like this:

ERCC-00002      37892   47258   42234   39986   25978   33998
ERCC-00003      2904    3170    3038    3488    2202    2680
ERCC-00004      910     1078    996     9200    6678    7396
ERCC-00009      638     778     708     1384    954     1108