├── LICENSE ├── R ├── Snakefile ├── gene_pipeline.R ├── misc.R ├── tcc2bootstrap.R ├── tcc_pipeline.R └── tx_pipeline.R ├── README.md ├── SRP091911 ├── R │ ├── gene_counts.R │ ├── tcc2bootstrap2.R │ ├── tcc_pipeline.R │ └── transcript_pipeline.R ├── Snakefile ├── make_batch_single.py └── simple_sample_table.txt ├── SRP100701 ├── R │ ├── GO_analysis.R │ ├── gene_pipeline.R │ ├── plot_pvalues.R │ ├── plot_transcripts.R │ ├── tcc2bootstrap.R │ ├── tcc_pipeline.R │ ├── tx_pipeline.R │ └── tximport.R ├── Snakefile ├── make_batch_single.py └── sample_table.txt └── simulation_pipeline ├── R ├── averaging_fdrs.R ├── gene_pipeline.R ├── mamabear.R ├── misc.R ├── null_sim.R ├── roc_curve.R ├── tcc2bootstrap.R ├── tcc_pipeline.R └── tx_pipeline.R ├── Snakefile └── make_batch.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/aggregationDE/HEAD/LICENSE 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