Bulk and signature data

[j-bac]

Many thanks for the insightful study and well-organized repo !

I downloaded the single cell datasets following the instructions and python script. However I am not sure how to obtain the bulk data and signatures. e.g. in configs/config_gbm_subsample.yml:

    bulk_path: TCGA_data/GBM/GBM_gex_fpkm_uq.csv
    signatures:
      - neftel_4
      - neftel_6




signatures:
  neftel_4:
    annotation_path: annotations/Neftel_4.csv
    scoring_scenario: neftel_smartseq2_brain
    n_cluster: 4

  neftel_6:
    annotation_path: annotations/Neftel_6.csv
    scoring_scenario: neftel_smartseq2_brain
    n_cluster: 6

[josephineyates]

Hello, sorry for the late reply!

For the bulk data you can directly download it from the UCSC Xena browser. We use FPKM UQ data.
For example, for GBM, you would download the FPKM UQ data from here: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

For the signatures, they are available from the original paper. For example, the Neftel et al. signatures are available here as Supplementary Table 2: https://www.sciencedirect.com/science/article/pii/S0092867419306877.

Hope this helps!