Files in jrboyd/seqtsne

Application of t-sne to NGS Genomic Signal Profiles

IKAROSchip_QC.jrb.R R/ChIPtSNE.R R/ClusteredSignal_TSNE.R R/ctPlots.R R/data_tsne.R R/function_plot_raster_summary.R R/functions_animation.R R/functions_cluster.R R/functions_fetch.R R/functions_image_rect.R R/functions_path.R R/functions_tsne.R R/functions_tsne_plots.R R/functions_tsne_plots_glyphs.R R/functions_util.R R/functions_velocity.R R/globals.R R/run_example.R README.md inst/shiny-examples/example_app/server.R inst/shiny-examples/example_app/setup.R inst/shiny-examples/example_app/ui.R man/ChIPtSNE.Rd man/ChIPtSNE.runTSNE.Rd man/ClusteredSignal_TSNE-class.Rd man/ClusteredSignal_TSNE.Rd man/ClusteredSignal_TSNE.fromConfig.Rd man/ClusteredSignal_TSNE.null.Rd man/ConfigFeatures.GRanges.Rd man/ConfigFeatures.Rd man/ConfigFeatures.files.Rd man/ConfigFeatures.parse.Rd man/ConfigFeatures.save_config.Rd man/ConfigSignal.Rd man/ConfigSignal.files.Rd man/aggregate_signals.Rd man/bam_pileup_dt.Rd man/bin_values.Rd man/bin_values_centers.Rd man/calc_delta.Rd man/combine_most_similar.Rd man/ctClusterPoints.Rd man/ctPlotBinAggregates.Rd man/ctPlotPoints.Rd man/ctPlotPointsAnnotation.Rd man/ctPlotSummaryProfiles.Rd man/fetch_bam_dt.Rd man/fetch_bam_stranded_dt.Rd man/fetch_bw_dt.Rd man/geom_image.rect.Rd man/hESC_data.Rd man/nn_clust.Rd man/plot_binned_aggregates.Rd man/plot_flat.Rd man/plot_outline.Rd man/plot_path.Rd man/plot_profiles_selected.Rd man/plot_recentered_velocity.Rd man/plot_regional_velocity.Rd man/plot_summary_glyph.Rd man/plot_summary_raster.Rd man/plot_summary_raster_byCell.Rd man/plot_velocity_arrows.Rd man/plot_velocity_bins.Rd man/plot_velocity_centered.Rd man/prep_images.Rd man/prep_profile_dt.Rd man/prep_query_gr.Rd man/prep_summary.Rd man/prep_velocity.Rd man/profile_dt.Rd man/query_gr.Rd man/rescale_capped.Rd man/runExample.Rd man/run_tsne.Rd man/sampleCap.Rd man/set_image_rects.Rd man/stsFetchTsneInput.Rd man/stsPlotClusterProfiles.Rd man/stsPlotSummaryProfiles.Rd man/tsne_dt.Rd presentation_figures.R tests/testthat.R tests/testthat/no_test/generate_test_data.R tests/testthat/no_test/test_cluster.R tests/testthat/no_test/test_fetch_bam.R tests/testthat/no_test/test_fetch_bw.R tests/testthat/no_test/test_image_summary.R tests/testthat/no_test/test_path.R tests/testthat/no_test/test_velocity.R tests/testthat/test_ssvTSNE.R vignettes/chiptsne_overview.Rmd