Files in jrboyd/seqtsne
Application of t-sne to NGS Genomic Signal Profiles
.Rbuildignore
.gitignore
DESCRIPTION
IKAROSchip_QC.jrb.R
LICENSE
NAMESPACE
NEWS
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_plots.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
chiptsne.Rproj
codecov.yml
data/bam_pileup_dt.rda
data/ex_cfg_dt.bam.rda
data/ex_cfg_dt.rda
data/ex_sts.rda
data/profile_dt.rda
data/query_gr.rda
data/tsne_dt.rda
inst/extdata/HUES48_H3K27me3_pooled.sorted.bam
inst/extdata/HUES48_H3K27me3_pooled_FE.bw
inst/extdata/HUES48_H3K4me3_pooled.sorted.bam
inst/extdata/HUES48_H3K4me3_pooled_FE.bw
inst/extdata/HUES48_input_pooled.sorted.bam
inst/extdata/HUES64_H3K27me3_pooled.sorted.bam
inst/extdata/HUES64_H3K27me3_pooled_FE.bw
inst/extdata/HUES64_H3K4me3_pooled.sorted.bam
inst/extdata/HUES64_H3K4me3_pooled_FE.bw
inst/extdata/HUES64_input_pooled.sorted.bam
inst/extdata/query_gr.bed
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/.gitignore
tests/testthat/dev_object.ssvQC.plotSignal.Rds
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
