This repository contains all scripts used for the analysis of differentially expressed genes in thyroid cancer samples with NTRK fusions.
- NTRK_all_fusion_samples.thyroid_cancer.csv - table with list of TCGA sample IDs with NTRK fusions
- deseq2_htseq_counts.R - R script that was used for the analysis of differentially expressed genes
- filterHtseqCounts.sh - bash script that was used for the intersection of transcript list for the tumor and normal tissue samples
- intersect_HTSeq_data.R - R script that was used for the intersection of transcript list for the tumor and normal tissue samples
- removeTranscriptVersions.sh - bash script that removes trascript version from the htseq-counts files
- Workflow_NTRK.dml - XML code of the workflow to analyze a gene set and to predict master-regulators. To execute, the workflow should be uploaded into genexplain platform https://platform.genexplain.com
- Workflow_NTRK.png - Block-diagram of the workflow to analyze a gene set and to predict master-regulators.