| File name | File content | Purpose |
|---|---|---|
| TME_gene_signatures | Gene signatures of macrophages and T-cells states | Help cell state annotation |
| METABRIC/tnbc_chemoYES.pat_names.txt | METABRIC patient ID that we used in our manuscript | Find the external cohort that is comparable to our cohort |
| SCANB/tnbc_chemoyes.id.txt | SCAN-B patient ID that we used in our manuscript | Find the external cohort that is comparable to our cohort |
| See here | Marker genes of the Vanderbilt TNBC subtypes | Pre-existing marker of TNBC subtypes |
| TNBC_Burstein2015 | Text file of the marker genes of the TNBC subtypes in the Burstein2015 study | Compare our archetypes with pre-existing TNBC subtypes |
| normal_breast_epithelial_lineage.gmx.csv | Top marker genes of the three normal epithelial lineages. | Investigating the epithelial lineage and cell-of-origin. |
| hbca_ref.sr3.rds | Single-cell RNA-seq data of a normal breast tissue from the HBCA project | Negative-control of performing copy number alteration inference |
| tnbc_solid_normal.se.rds and tnbc_primary_tumor.se.rds | Bulk RNA-seq data of normal and tumor samples of BRCA from the TCGA project | Possible negative & positive-controls to facilitate copy number alteration inference |
| DiffusionMap | Reference data objects of the epithelial cells from the Human Breast Cell Atlas data | Run Diffusion Map analysis on the cancer cells only |
| BrighTNess | Text file of the patient or sample IDs | Subset the data from the original study to provide the TNBC cohort comparable to our study |
| ISPY990 | Text file of the patient or sample IDs | Subset the data from the original study to provide the TNBC cohort comparable to our study |
| SCTD | Reference data objects of 1) the Human Breast Cell Atlas data and 2) the TNBC tumor tissue data | Run the RCTD analysis on the Visium HD data |
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