TE analysis in CRC

This is the main codes for analysis TE signature in CRC

'work.flow_get_candidate_TEs.R' contains main scripts for candidate TEs.

'clin.data.CRC.selected.R' is main script for CRC sample selection.

Folder under '2.survival.TE.screen' contains the analysis of survival-associated TEs.

Folder under '3.immu.correlated/stat.20200405' contains the analysis of immune-associated TEs.

Folder under '4.model' contains the analyis based on identification of TE clusters.

Folder under '5.TE.cor.with.gene' is for identification of genes correlated with TE score.

Folder under '9.AZAdata.GBM' is for analysis of DNA methylation inhibitors treated cell lines data.

Folder under 'scRNA' is for identification of transcriptomes and TE expression in scRNA.

'run.java.gsea.TE4vsother.sh' is the script for gsea analysis.