Technical Help sheet

Technical requirements for data analysis

You will require the following tools for executing the practicals in this course:

Introduction to R programming; Data visualisation and plotting using ggplot2; Organising your work with R projects and version control (Git)

R studio
Visual Studio Codehttps://code.visualstudio.com/
Git
R packages: ggplot2, dplyr, patchwork, Seurat, SeuratData

B/T cell receptor analysis

R packages: tidyverse
Git
MIXCRhttps://mixcr.com/
arcasHLAhttps://github.com/RabadanLab/arcasHLA
Web Browser (preferably chrome)

Bulk RNA-seq and Single cell RNA-seq

Git
R 4.0.3https://cran.r-project.org/
R studiohttps://www.rstudio.com/products/rstudio/download/#download
tidyversehttps://cran.r-project.org/web/packages/tidyverse/index.html
airwayhttps://bioconductor.org/packages/release/data/experiment/html/airway.html
DESeq2https://bioconductor.org/packages/release/bioc/html/DESeq2.html
edgeRhttps://bioconductor.org/packages/release/bioc/html/edgeR.html
limmahttps://bioconductor.org/packages/release/bioc/html/limma.html
patchworkhttps://cran.r-project.org/web/packages/patchwork/index.html
knitrhttps://cran.r-project.org/web/packages/knitr/index.html
markdownhttps://cran.r-project.org/web/packages/markdown/index.html
Seurathttps://cran.r-project.org/web/packages/Seurat/index.html
futurehttps://cran.r-project.org/web/packages/future/index.html
DoubletFinderhttps://github.com/chris-mcginnis-ucsf/DoubletFinder
clustreehttps://cran.r-project.org/web/packages/clustree/index.html
svahttps://bioconductor.org/packages/release/bioc/html/sva.html
fgseahttp://bioconductor.org/packages/release/bioc/html/fgsea.html
singleCellNethttps://github.com/pcahan1/singleCellNet
vsnhttps://bioconductor.org/packages/release/bioc/html/vsn.html
AnnotationDbihttps://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html
org.Hs.eg.dbhttps://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
apeglmhttps://bioconductor.org/packages/release/bioc/html/apeglm.html
pheatmaphttps://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf
ggrepelhttps://cloud.r-project.org/web/packages/ggrepel/index.html
MuSiChttps://github.com/xuranw/MuSiC
WGCNAhttps://cran.r-project.org/web/packages/WGCNA/index.html
SeuratDatahttps://github.com/satijalab/seurat-data
SeuratDiskhttps://github.com/mojaveazure/seurat-disk
all dependencies from the above R packages
python and leidenalghttps://github.com/vtraag/leidenalg

Introduction to flow cytometry and flow cytometry data analysis

R
R studio
R packages: dplyr, ggplot2, tidyr, markdown, devtools, flowCore, ggpubr, pheatmap, FlowSOM, PeacoQC, CytoNorm, flowDensity, ggpointdensityhttps://github.com/LKremer/ggpointdensity, https://github.com/saeyslab/CytoNorm, https://github.com/saeyslab/FlowSOM, https://github.com/saeyslab/PeacoQC

EMBL-EBI resources

Web Browser (preferably chrome)
Expression Atlas webpagehttps://www.ebi.ac.uk/gxa/home
Single cell Expression Atlas webpagehttps://www.ebi.ac.uk/gxa/sc/home
Ensembl webpagehttps://www.ensembl.org/
IntAct webpagehttps://www.ebi.ac.uk/intact/home
Reactome webpagehttps://reactome.org/