added scripts for publication

GrAnnoT/codes4publications/README.md

GrAnnoT/codes4publications/TE_IT_liftoff_grannot.ipynb

GrAnnoT/codes4publications/TE_IT_rates.R

GrAnnoT/codes4publications/applications.py

GrAnnoT/codes4publications/compare_double_transfer.ipynb

GrAnnoT/codes4publications/compare_genome_transfers.ipynb

GrAnnoT/codes4publications/compare_genome_transfers_upset.R

GrAnnoT/codes4publications/compare_graph_ref.ipynb

GrAnnoT/codes4publications/compare_graph_transfers.ipynb

GrAnnoT/codes4publications/compare_graph_transfers_upset.R

.../codes4publications/compare_liftoff_grannot_species.ipynb

GrAnnoT/codes4publications/compare_time_12transfers.R

GrAnnoT/codes4publications/liftOffChainer.sh

GrAnnoT/codes4publications/variation_rate_per_feature_type.R