Scripts
Clicking on a script in the table below should open a download window. Some browsers or browser configurations may block this activity. If you have trouble downloading the scripts below, please try a different browser. Alternatively, you can right/control click on the link below and choose ‘Copy Link Address’. Open a new browser tab or window, paste in this copied URL, hit return, and the download window should pop-up.
| Script Name | Packages | Last updated |
|---|---|---|
| Step1_TxImport.R | tximport, tidyverse, biomaRt, ensemblDB | April 10th 2024 |
| Step2_dataWrangling.R | ggplot2, tidyr, matrixstats, edgeR | April 10th 2024 |
| Step3_multivariate.R | ggplot2, tidyverse, plotly, gt, DT | April 10th 2024 |
| Step4_publicData.R | rhdf5 | April 10th 2024 |
| Step5_diffGenes.R | limma, edgeR, SVA | April 10th 2024 |
| Step6_modules.R | gplots, Rcolorbrewer, heatmaply, d3heatmap | April 10th 2024 |
| Step7_functionalEnrichment.R | GSVA, gprofiler2, clusterProfiler, msigdbr, enrichplot | April 10th 2024 |
| Step8_essentials.R, Rmarkdown_template.Rmd, Rmarkdown_essentials.Rmd, flexdashboard_essentials.Rmd | Rmarkdown, Knitr, renv, flexdashboard | April 10th 2024 |
| buildPkg.R | devtools, usethis, roxygen2 | April 10th 2024 |
| DIY_scRNAseq.R | Seurat, DropletUtils, Scater, SingleR, celldex | April 10th 2024 |