├── LICENSE ├── README.md ├── TEProf2.yml └── bin ├── aggregateProcessedAnnotation.R ├── annotationtpmprocess.py ├── arguments.txt ├── commandsmax_speed.py ├── commandsmax_speed_se.py ├── filterReadCandidates.R ├── finalStatisticsOutput.R ├── genecode_introns.py ├── genecode_to_dic.py ├── mergeAnnotationProcess.R ├── mergeAnnotationProcess_Ref.R ├── rmsk_annotate_bedpe_speed.py ├── rmsk_annotate_bedse_speed.py ├── rmskhg38_annotate_gtf_update_test_tpm.py ├── rmskhg38_annotate_gtf_update_test_tpm_cuff.py ├── run_pipeline.sh ├── run_pipeline_rf.sh ├── stringtieExpressionFrac.py ├── translationPart1.R └── translationPart2.R /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/twlab/TEProf2Paper/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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