Man pages for jrboyd/seqtsne
Application of t-sne to NGS Genomic Signal Profiles
| aggregate_signals | aggregate_signals |
| bam_pileup_dt | data.table of bam pileups |
| bin_values | bin_values |
| bin_values_centers | bin_values_centers |
| calc_delta | calc_delta |
| ChIPtSNE | ChIPtSNE |
| ChIPtSNE.runTSNE | ChIPtSNE.runTSNE |
| ClusteredSignal_TSNE | ClusteredSignal_TSNE |
| ClusteredSignal_TSNE-class | ClusteredSignal_TSNE |
| ClusteredSignal_TSNE.fromConfig | ClusteredSignal_TSNE.fromConfig |
| ClusteredSignal_TSNE.null | ClusteredSignal_TSNE.null |
| combine_most_similar | combine_most similar |
| ConfigFeatures | QcConfigFeatures |
| ConfigFeatures.files | QcConfigFeatures |
| ConfigFeatures.GRanges | QcConfigFeatures.GRanges |
| ConfigFeatures.parse | QcConfigFeatures |
| ConfigFeatures.save_config | QcConfigFeatures |
| ConfigSignal | QcConfigSignal |
| ConfigSignal.files | QcConfigSignal |
| ctClusterPoints | ctClusterPoints |
| ctPlotBinAggregates | ctPlotBinAggregates |
| ctPlotPoints | ctPlotPoints |
| ctPlotPointsAnnotation | ctPlotPointsAnnotation |
| ctPlotSummaryProfiles | ctPlotSummaryProfiles |
| fetch_bam_dt | fetch_bam_dt |
| fetch_bam_stranded_dt | fetch_bam_stranded_dt |
| fetch_bw_dt | fetch_bw_dt |
| geom_image.rect | geom_image.rect |
| hESC_data | Data from 3 hESC cell lines for two histone modifications,... |
| nn_clust | nn_clust |
| plot_binned_aggregates | plot_binned_aggregates |
| plot_flat | plot_flat |
| plot_outline | plot_outline |
| plot_path | plot_path |
| plot_profiles_selected | plot_profiles_selected |
| plot_recentered_velocity | plot_recentered_velocity |
| plot_regional_velocity | plot_regional_velocity |
| plot_summary_glyph | plot_summary_glyph |
| plot_summary_raster | plot_summary_raster |
| plot_summary_raster_byCell | plot_summary_raster_byCell |
| plot_velocity_arrows | plot_velocity_arrows |
| plot_velocity_bins | Title |
| plot_velocity_centered | plot_velocity_centered |
| prep_images | prep_images |
| prep_profile_dt | applies normalizations and transformations to prof_dt, a tidy... |
| prep_query_gr | prepares query_gr GRanges for using in fetch functions |
| prep_summary | prep_summary |
| prep_velocity | prep_velocity |
| profile_dt | data.table of fold-enrichment |
| query_gr | GRanges region annotation of hESC bivalent sites. |
| rescale_capped | wraps scales::rescale to enforce range of 'to' on output |
| runExample | runExample |
| run_tsne | run_tsne |
| sampleCap | sampleCap |
| set_image_rects | set_image_rects |
| stsFetchTsneInput | stsFetchTsneInput |
| stsPlotClusterProfiles | stsPlotClusterProfiles |
| stsPlotSummaryProfiles | stsPlotSummaryProfiles |
| tsne_dt | data.table of tsne embedding |
