Resources to learn R
- When using R, use Rstudio, the great development environment.
- RStudio: https://rstudio.com/
- R: https://cran.r-project.org/
- Bioconductor and CRAN are two major R package repositories. Bioconductor is more specific to genetic and genomic data analyses while CRAN is for more general statistical analyses.
- Bioconductor: https://bioconductor.org/
- CRAN: https://cran.r-project.org/
- Collection of introductory documents can be found here: https://cran.r-project.org/other-docs.html
- ggplot2 is the most popular and cutting edge visualization tool: https://ggplot2.tidyverse.org/
- pheatmap is the great R package to generate heatmaps: https://cran.r-project.org/web/packages/pheatmap/index.html
- plotly is the even more cutting edge visualization tool that allows dynamic and interactive visualization: https://plotly.com/r/
- UMAP and tSNE are embedded in mulitple software but if you want to play with them, you can try the following R packages.
- UMAP: https://cran.r-project.org/web/packages/umap/vignettes/umap.html
- tSNE: https://cran.r-project.org/web/packages/Rtsne/index.html
- edgeR and DESeq2 are the most popular analysis methods for bulk RNA-seq.
- edgeR: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
- DESeq2: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
- Seurat and monocle are the most popular methods for visualization/clustering and pseudotime analyses, respectively, using single-cell RNA-seq data.
- Seurat: https://satijalab.org/seurat/
- Monocle: http://cole-trapnell-lab.github.io/monocle-release/
- Annotating cell types (singleR): https://bioconductor.org/packages/release/bioc/vignettes/SingleR/inst/doc/SingleR.html
- Orchestrating Single-Cell Analysis with Bioconductor: https://osca.bioconductor.org/
- TCR-seq data analysis tools are still under development in my impression. tcR has been popular for a while and immunarch is an emerging powerful tool for TCR-seq data analysis.
- immunarch: https://immunarch.com/
- tcR: https://cran.r-project.org/web/packages/tcR/vignettes/tcrvignette.html