Man pages for CshlSiepelLab/DENR
Deconvolution of Expression for Nascent RNA Sequencing Data
| add_data | Add data |
| apply_bigwig_seqinfo | Apply seqinfo from bigwig to GRanges |
| apply_shape_profile | Change shape of transcript models Create a... |
| assert_chromosome_exists | Assert chromosome exists |
| cache_create_dir | Create local cache |
| cache_defaults | Create cache defaults |
| cache_get_dir | Get local cache path |
| cache_set_dir | Set local cache path |
| collect_tss_features | Generate GRangesList of windows |
| covered_bases | Gets per-query coverage |
| create_bins | Create bins for multiple groups of overlapped transcripts |
| create_model_masks | Create model masks |
| create_transcript_models | Create transcript models |
| download_txdb | Download transcript model from biomart |
| fit | Fit model |
| gene_abundance | View gene abundances |
| get_abundance | retrieve abundance for plotting |
| get_data | Get data |
| get_masks | Get target masks |
| get_transcribed_regions | Annotates transcribed regions |
| get_transcripts | Get target transcripts |
| get_tx_id | get_tx_id |
| group_trancript_models | Group transcripts |
| group_transcripts | Group transcripts |
| is_length_two_vector | is_length_two_vector |
| is_matrix_list | is_matrix_list |
| is_strand_vector | is_strand_vector |
| is_vector_list | is_vector_list |
| labeled_feature_set | Build labeled data set |
| label_transcripts | Generate training labels for TSS |
| list_cached_txdb | View cache |
| load_txdb | Load txdb from cache |
| locus_statistics | locus_statistics |
| locus_variance_explained | locus_variance_explained |
| mask_data | Mask data |
| mask_transcripts | Mask transcripts |
| matrix_list_dim_equal | matrix_list_dim_equal |
| model_agreement | Computes GOF statistic for groups of transcripts |
| plot_model | Plot transcript_abundance object |
| predict_inactive_transcripts | Return list of inactive TSS |
| predict_locus | Predicts signal at locus level |
| predict_transcripts | predict_transcripts |
| reduce_transcript_models | Reduce transcript models |
| rescale_fixed_width_position | Tripartite linear rescaling |
| save_txdb | Cache a TxDb |
| seqv | Vectorized seq.default |
| set_datatrack_ylim | Set datatrack ylim |
| show-transcript_quantifier-method | Show an Object |
| split_path | Split path |
| strip_loess | Slims down loess object Removes parts of 'loess' object that... |
| summarize_bigwig | Summarize bigwig |
| sum_squares_grad | Sum of squares gradient |
| sum_squares_lasso | Sum of squares |
| total_coverage | Total coverage |
| transcript_abundance | View transcript abundances |
| transcript_quantifier | transcript_quantifier |
| transcript_quantifier-class | Class transcript_quantifier |
| transcript_quantifier_valid | transcript_quantifier_valid |
| transcript_shape_profile | Creates transcript_shape_profile |
| transcript_shape_profile-class | Class transcript_shape_profile |
| tss_predictor | Train TSS activity predictor |
| tx_variance_explained | tx_variance_explained |
| upstream_polymerase_ratio | density ratio calculation |
| view | View transcript shape profile View transcript shape model... |
| view_available_txdb | Retrieve ensembl biomart |
| window_regions | Generate GRangesList of windows |
