Chapter 6 Standalone analyses

6.1 BayesPrism

BayesPrism performs immune deconvolution of a TPM matrix using a single-cell reference.

iobrpy bayesprism \
  --input results/PRJDB16684/03-tpm/tpm_matrix.csv \
  --output results/PRJDB16684/08-bayesprism \
  --threads 4

The output directory contains:

results/PRJDB16684/08-bayesprism/
├── theta.csv
├── theta_cv.csv
└── Z_tumor.csv

6.2 TME clustering

TME clustering groups samples according to their tumor microenvironment profiles.

mkdir -p results/PRJDB16684/09-tme-cluster

iobrpy tme_cluster \
  --input results/PRJDB16684/05-tme/cibersort_results.csv \
  --output results/PRJDB16684/09-tme-cluster/tme_clusters.csv \
  --features 1:22 \
  --min_nc 2 \
  --max_nc 5 \
  --print_result

6.3 HLA typing

iobrpy hla_typing \
  -b results/PRJDB16684/02-star \
  -r hg38 \
  -o results/PRJDB16684/10-hla \
  -j 4 \
  -u 1

The output directory contains:

results/PRJDB16684/10-hla/
├── ExtractHLAread/<sample>/
├── SpecHLA/<sample>/hla.result.txt
└── hla_result_merged.txt