Eckart stolle (LIB Museum Koenig) Lars Podsiadlowski (LIB Museum Koenig) Katja Nowick (FU Berlin) Joe Colgan (U Mainz)
Day1: RNAseq, read processing, mapping, read counts, DEG, GO term enrichment (E. Stolle, L. Podsiadlowski, J. Colgan)
- Terminal which can do ssh, e.g. WSL, Git bash, PuttY, mobaXterm
- FileZilla or another equivalent tool to transfer remote files (if you are not using trynsfer via ssh (eg rsync)
- Rstudio
- Server: ssh -X -p 6022 [email protected]
For the purpose of this tutorial, there are some packages, which each of you will need to install. You can do so using the following commands:
# install bioconductor
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.18")
BiocManager::install(c("BiocFileCache","xml2","AnnotationDbi","XML","httr","KEGGREST","lintr","lattice","Rgraphviz"))
BiocManager::install("biomaRt")
BiocManager::install("topGO")
BiocManager::install("tximport")
BiocManager::install("tidyverse")
BiocManager::install("eulerr")
BiocManager::install("pheatmap")
BiocManager::install("RColorBrewer")
BiocManager::install("DESeq2")
install.packages('CoDiNA')
install.packages("devtools")
install.packages("ncdf4")
install.packages(c("HiClimR","igraph"))
library(devtools)
install_github("deisygysi/wTO")
devtools::install_github('RfastOfficial/Rfast')
install.packages("gplots")
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