1. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?

acc=GSE117988
read csv matrix

PBMC – control

Tumor – cancer

2. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123904
read csv matrix

control
MSK_LX684_NORMAL

MSK_LX685_NORMAL

Tumor

MSK_LX684_PRIMARY_TUMOUR

MSK_LX682_PRIMARY_TUMOUR

3. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE249361

read Barcode, feature and matrix from 10x (included).

control

Sample 9-P nonmalignant

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7937492

Sample 11-P nonmalignant

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7937496

cancer

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7937491
Sample 9-T

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7937495
Sample 11-T

4. small single cancer data (no control)

https://www.dropbox.com/sh/phkw22dvjafh16y/AACH_9_1nCb4hD4WrtB2SWwoa?dl=1
https://www.nature.com/articles/nature19328
database https://www.weizmann.ac.il/sites/3CA/

Minimum requirement for analysis

1. code
2. all UMAPs
3. cluster plot, and/or cell type plot (when annotation possible/required)
4. comparison of clusters and/or cell types of cancer tissue
5. across (non-cancer vs cancer, if applicable depending on DA question) and within (cancer cell
type/cluster vs cancer cell type/cluster) markers
6. GO of the markers
7. Top 5 to 10 markers search in Pubmed and google scholar and write hypothesis about them
8. All references/citation
9. GO term explanation and hypothesis