# R packages

## List of R packages used

### CRAN

* data.table: [https://cran.r-project.org/package=data.table](https://cran.r-project.org/package=data.table)
* dplyr: [https://cran.r-project.org/package=dplyr](https://cran.r-project.org/package=dplyr)
* reshape2: [https://cran.r-project.org/package=reshape2](https://cran.r-project.org/package=reshape2)
* ggplot2: [https://cran.r-project.org/package=ggplot2](https://cran.r-project.org/package=ggplot2)
* ggrepel: [https://cran.r-project.org/package=ggrepel](https://cran.r-project.org/package=ggrepel)
* ggbeeswarm: [https://cran.r-project.org/package=ggbeeswarm](https://cran.r-project.org/package=ggbeeswarm)

### Bioconductor

* GenomicFeatures: [https://bioconductor.org/packages/GenomicFeatures/](https://bioconductor.org/packages/GenomicFeatures/)
* tximport: [https://bioconductor.org/packages/tximport/](https://bioconductor.org/packages/tximport/)
* DESeq2: [https://bioconductor.org/packages/DESeq2/](https://bioconductor.org/packages/DESeq2/)
* apeglm: [https://bioconductor.org/packages/apeglm/](https://bioconductor.org/packages/apeglm/)
* EnhancedVolcano: [https://bioconductor.org/packages/EnhancedVolcano/](https://bioconductor.org/packages/EnhancedVolcano/)
* DRIMSeq: [https://bioconductor.org/packages/DRIMSeq/](https://bioconductor.org/packages/DRIMSeq/)
* DEXSeq: [https://bioconductor.org/packages/DEXSeq/](https://bioconductor.org/packages/DEXSeq/)
* stageR: [https://www.bioconductor.org/packages/stageR/](https://www.bioconductor.org/packages/stageR/)
* edgeR: [https://www.bioconductor.org/packages/edgeR/](https://www.bioconductor.org/packages/edgeR/)

### GitHub

* wasabi: [https://github.com/COMBINE-lab/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](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")
```
