├── .gitignore ├── .lintr ├── CHANGELOG.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── bootstrap.R ├── gene_analysis.R ├── hexamers.R ├── import.R ├── kallisto.R ├── likelihood.R ├── matrix.R ├── measurement_error.R ├── misc.R ├── model.R ├── plots.R ├── read_write.R ├── shiny.R ├── sleuth.R └── units.R ├── README.md ├── inst ├── doc │ └── intro.html └── scripts │ ├── gen_hexamers.sh │ └── hexamers.py ├── man ├── basic_filter.Rd ├── cash-set-.sleuth.Rd ├── design_matrix.Rd ├── excluded_ids.Rd ├── extract_model.Rd ├── gene_from_gene.Rd ├── get_bootstrap_summary.Rd ├── get_bootstraps.Rd ├── get_col.Rd ├── is_kallisto_subset.Rd ├── kallisto_table.Rd ├── log_transform.Rd ├── models.Rd ├── norm_factors.Rd ├── plot_bootstrap.Rd ├── plot_fld.kallisto.Rd ├── plot_fld.sleuth.Rd ├── plot_group_density.Rd ├── plot_loadings.Rd ├── plot_ma.Rd ├── plot_mean_var.Rd ├── plot_pc_variance.Rd ├── plot_pca.Rd ├── plot_qq.Rd ├── plot_sample_density.Rd ├── plot_sample_heatmap.Rd ├── plot_scatter.Rd ├── plot_transcript_heatmap.Rd ├── plot_vars.Rd ├── plot_volcano.Rd ├── print.sleuth_model.Rd ├── read_kallisto.Rd ├── read_kallisto_h5.Rd ├── read_kallisto_tsv.Rd ├── sleuth_deploy.Rd ├── sleuth_fit.Rd ├── sleuth_gene_table.Rd ├── sleuth_live.Rd ├── sleuth_live_settings.Rd ├── sleuth_load.Rd ├── sleuth_lrt.Rd ├── sleuth_prep.Rd ├── sleuth_results.Rd ├── sleuth_save.Rd ├── sleuth_to_matrix.Rd ├── sleuth_wt.Rd ├── subset_kallisto.Rd ├── transcripts_from_gene.Rd ├── transform_fun_counts-set.Rd ├── transform_fun_tpm-set.Rd ├── transform_status.Rd └── write_kallisto_hdf5.Rd ├── tests ├── testthat.R └── testthat │ ├── ellahi │ ├── README.md │ ├── SRR1811834 │ │ └── kallisto │ │ │ └── abundance.h5 │ ├── SRR1812754 │ │ └── kallisto │ │ │ └── abundance.h5 │ ├── SRR1812759 │ │ └── kallisto │ │ │ └── abundance.h5 │ ├── SRR1812760 │ │ └── kallisto │ │ │ └── abundance.h5 │ ├── SRR1812767 │ │ └── kallisto │ │ │ └── abundance.h5 │ ├── SRR1812768 │ │ └── kallisto │ │ │ └── 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