basic_filter | Basic row filter |
cash-set-.sleuth | Extend internal '$<-' for sleuth object |
design_matrix | Extract design matrix |
excluded_ids | Excluded IDs in Kallisto object |
extract_model | Extract a model from a sleuth object |
gene_from_gene | Get the gene ID using other gene identifiers |
get_bootstraps | Extract bootstrap for a specific transcript |
get_bootstrap_summary | bootstrap summary |
get_col | Get a data.frame from all kallisto objects |
is_kallisto_subset | Is Kallisto Object Subsetted? |
kallisto_table | Get kallisto abundance table from a sleuth object |
log_transform | Natural log and offset transformation |
models | View which models have been fit |
norm_factors | Normalization factors |
plot_bootstrap | Plot bootstrap summary |
plot_fld.kallisto | Plot fragment length distribution |
plot_fld.sleuth | Plot fragment length distribution |
plot_group_density | Plot density |
plot_loadings | Plot Loadings and Interpretations |
plot_ma | MA plot |
plot_mean_var | Mean-variance relationship |
plot_pca | Plot PCA |
plot_pc_variance | Plot PC Variance |
plot_qq | QQ plot |
plot_sample_density | Plot sample density |
plot_sample_heatmap | Plot sample heatmap |
plot_scatter | Sample to sample scatter plot |
plot_transcript_heatmap | Plot clustered heatmap |
plot_vars | Plot technical variance versus observed variance |
plot_volcano | Plot volcano plot |
print.sleuth_model | Print sleuth model |
read_kallisto | Read kallisto output |
read_kallisto_h5 | Read a kallisto object from an HDF5 file |
read_kallisto_tsv | Read kallisto plaintext output |
sleuth_deploy | deploy a sleuth object |
sleuth_fit | Fit a measurement error model |
sleuth_gene_table | Create a gene table from a sleuth object |
sleuth_live | Interactive sleuth visualization with Shiny |
sleuth_live_settings | settings for sleuth_live |
sleuth_load | load a sleuth object |
sleuth_lrt | sleuth likelihood ratio test |
sleuth_prep | Constructor for a 'sleuth' object |
sleuth_results | Extract Wald or Likelihood Ratio test results from a sleuth... |
sleuth_save | save a sleuth object |
sleuth_to_matrix | Convert a sleuth object to matrix |
sleuth_wt | Wald test for a sleuth model |
subset_kallisto | Subset a kallisto object |
transcripts_from_gene | Get the names of the transcripts associated to a gene |
transform_fun_counts-set | Change sleuth transform counts function |
transform_fun_tpm-set | Change sleuth transform TPM function |
transform_status | Check Transform Sync Status of Sleuth Fits |
write_kallisto_hdf5 | Write a kallisto object to HDF5 |
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