title: "2021 Fasting Cancer Project"

author: "Charlie Whittaker"

date: "1/19/2021 - revised July 2024"

output:

html_document: default

html_notebook: default

```{r setup, include=FALSE}

```{r, warning=FALSE,error=FALSE,message=FALSE}

the initial processing was done with r 3.6.1 with Seurat 3.2.0 - the UMAP comes out slightly differently in r 4.0.3 with Seurat 3.2.3*

NOTE: loading final object to avoid recalculating ssGSEA data

```{r, fig.width=14, fig.height=10}

```{r, fig.width=14, fig.height=10}

```{r, fig.width=14, fig.height=8}

```{r, fig.width=12, fig.height=10}

This code is no longer working due to R and package updates but resulting data is stored in the seurat object

escape 1.0.0 is probably required but is no longer available. the version in this R image is 1.0.1

escape ssGSEA - run ssGSEA to quantify expression of the BitonI gene set clusters

Figure 5G - Biton 1 in cluster5*

Figure 5G_II - Biton II in cluster2*

Figure 5G_III - Biton III in cluster10*

Figure 5H - Pdgfa in cluster5*

Figure S3E - Gkn3 in cluster5*