Man pages for pachterlab/sleuth
Tools for investigating RNA-Seq
| 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 |
