Resources

RT

2022-05-18

Useful packages:

Clean up code

formatR

Update R

updateR

Interactive visualization:

plotly ggplotly Glimma

nice tables in Rmarkdown

DT

Enrichment analysis

clusterProfiler

Annotation of genomic regions

annotatr

Gene expression (RNASeq) analysis

DESeq2 EdgeR

Mutation data

MAFtools

Visualization genomic regions

Gviz

Handling genomic data (e.g. bam files)

rtracklayer

Methylation data

Array

minfi RnBeads

Sequencing

methrix bsseq

Visualization, heatmaps

pheatmap Complexheatmap

Circular plots

circlize

Upset plot

upsetR

Alluvial plot

ggalluvial

Nice colors palettes

ggsci scico

All color palettes

Cheatsheets

Cheatsheets

Awesome R

Awesome