How-To R

Please add your how-tos.

R and RStudio

R is a widely used statistical package, most likely you will want to run R through RStudio.

  1. Install R: download from one of the mirrors listed under USA on this page https://cran.r-project.org/mirrors.html. The R package updates frequently (significant updates every month or two). The packages that you actually use, e.g., Bioconductor, DESeq2, usually update more slowly so they may not work in the most current version of R. Make sure the packages you want to use have been updated (should be in the vignette). I usually don't update until 6-12 months after a new version is released gribskovgribskov
  2. Install RStudio: download RStudio desktop from https://posit.co/downloads/

My plan is to add the entire DESeq2 procedure as a series of pages (or a single page with collapsible sections) all beginning DESeq2-. The single complete file is very long and has a variety of options. gribskovgribskov 2022-11-6

Available Pages

DESeq2 - overview - gribskov - 21 Nov 2022 16:53
GO term analysis with topGO - gribskov - 21 Nov 2022 15:43
DESeq2 - initial normalization - gribskov - 09 Nov 2022 01:03
ggplot2 - count density plot - gribskov - 09 Nov 2022 00:49
ggplot2 - data box plot - gribskov - 08 Nov 2022 20:24
DESeq2 - read data - gribskov - 08 Nov 2022 20:13
update R - gribskov - 06 Nov 2022 11:29
ggplot2 - overlapping density plots - gribskov - 06 Nov 2022 11:26
kmers with pure R - gribskov - 06 Nov 2022 11:19
extreme value distribution - gribskov - 06 Nov 2022 11:16
bioconductor initialization - gribskov - 06 Nov 2022 11:10
How-To R - gribskov - 05 Nov 2022 23:31

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