> For the complete documentation index, see [llms.txt](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/preparations/r-packages.md).

# R packages

## List of R packages used

### CRAN

* data.table: <https://cran.r-project.org/package=data.table>
* dplyr: <https://cran.r-project.org/package=dplyr>
* reshape2: <https://cran.r-project.org/package=reshape2>
* ggplot2: <https://cran.r-project.org/package=ggplot2>
* ggrepel: <https://cran.r-project.org/package=ggrepel>
* ggbeeswarm: <https://cran.r-project.org/package=ggbeeswarm>

### Bioconductor

* GenomicFeatures: <https://bioconductor.org/packages/GenomicFeatures/>
* tximport: <https://bioconductor.org/packages/tximport/>
* DESeq2: <https://bioconductor.org/packages/DESeq2/>
* apeglm: <https://bioconductor.org/packages/apeglm/>
* EnhancedVolcano: <https://bioconductor.org/packages/EnhancedVolcano/>
* DRIMSeq: <https://bioconductor.org/packages/DRIMSeq/>
* DEXSeq: <https://bioconductor.org/packages/DEXSeq/>
* stageR: <https://www.bioconductor.org/packages/stageR/>
* edgeR: <https://www.bioconductor.org/packages/edgeR/>

### GitHub

* wasabi: <https://github.com/COMBINE-lab/wasabi>

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("devtools")    # only if devtools not yet installed
BiocManager::install("COMBINE-lab/wasabi")
```

* sleuth: <https://github.com/pachterlab/sleuth>

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("devtools")    # only if devtools not yet installed
BiocManager::install("pachterlab/sleuth")
```