Tumor Immune and Stromal Microenvironment (TISME) 10x Multiome metacell atlas

• Benchmark the construction of the TISME 10x multiome (RNA+ATAC) metacell atlas with semi-supervised and unsupervised workflows using our metacell tool SuperCell2.0 and STACAS.
• Annotate and analyze the semi-supervised multimodal TISME 10x multiome metacell atlas.

Input count matrix

This work is based on 10x multiome data previously generated and analysed at the single level in Terekhanova et al..

The workflow requires RNA and ATAC count matrices, as well as coarse cell annotations and ATAC fragment files from the Human Tumor Atlas Network HTAN atlas. These data can be download through synapse.

Additional data

Additional data (eg. containers, transcription factor motifs pfm matrix, gene signatures from the literature) required for this workflow are availbale on zenodo

Snakemake command:

snakemake --snakefile Snakefile_final.py --profile slurm/ --configfile config_files/multiome_data_analysis/config.yaml