Showcasing coding for variant calling, python, ATACseq, cellbender and spatial transcriptomics,
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FGA_TMB: it contains an R script for calculating FGA and TMB in Wilms tumor project. It also contains a bash script pipeline of GATK-based somatic short mutations (SSM) calling that is required for TMB (nonsynonymous mutations). The result of SSM calling can be accessed on UCSC GB.
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python_scripts: it contains some python scripts from different projects j.ipynb and j.py are from PDAC tropism repository (scripts/Fig_4) API.py from EnrichR repository mtx2loom.py from veloPipe repository
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shell_scripts_pipeline_ATACseq: it contains bash scripts of ATAC-seq pipeline. These are from the ATACseq repository.
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shell_scripts_pipeline_cellbender: it contains bash scripts of cellbender (denoising snRNAseq data) pipeline
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spatial_transcriptomics: it contains scripts for RCTD-based deconvolution of spatial transcriptome sequencing data in the PDAC tropism project (scripts/Fig_4)