Files in jrboyd/seqsetvis

Set Based Visualizations for Next-Gen Sequencing Data

R/annotate_subject_GR.R R/data_info_CTCF.R R/data_info_chromHMM.R R/functions_clusteringKmeans.R R/functions_easyLoad.R R/functions_exon_signal.R R/functions_feature_plots.R R/functions_fetch_GRanges.R R/functions_fetch_bam.R R/functions_fetch_bamPE.R R/functions_fetch_bamPE_RNA.R R/functions_fetch_bigwig.R R/functions_fetch_signal.R R/functions_fragLen.R R/functions_normalization.R R/functions_signal_operations.R R/functions_signal_plots.R R/misc_helpers.R R/overlapIntervalSets.R R/seqsetvis.R R/ssvMakeMembTable.R README.md man/Bcell_peaks.Rd man/CTCF_in_10a_bigWig_urls.Rd man/CTCF_in_10a_data.Rd man/CTCF_in_10a_narrowPeak_grs.Rd man/CTCF_in_10a_narrowPeak_urls.Rd man/CTCF_in_10a_overlaps_gr.Rd man/CTCF_in_10a_profiles_dt.Rd man/CTCF_in_10a_profiles_gr.Rd man/add_cluster_annotation.Rd man/append_ynorm.Rd man/applyMovingAverage.Rd man/applySpline.Rd man/assemble_heatmap_cluster_bars.Rd man/calc_norm_factors.Rd man/centerAtMax.Rd man/centerFixedSizeGRanges.Rd man/centerGRangesAtMax.Rd man/chromHMM_demo_bw_states_gr.Rd man/chromHMM_demo_chain_url.Rd man/chromHMM_demo_data.Rd man/chromHMM_demo_overlaps_gr.Rd man/chromHMM_demo_segmentation_url.Rd man/chromHMM_demo_state_colors.Rd man/chromHMM_demo_state_total_widths.Rd man/clusteringKmeans.Rd man/clusteringKmeansNestedHclust.Rd man/col2hex.Rd man/collapse_gr.Rd man/convert_collapsed_coord.Rd man/copy_clust_info.Rd man/crossCorrByRle.Rd man/dot-expand_cigar_dt.Rd man/dot-expand_cigar_dt_recursive.Rd man/dot-rm_dupes.Rd man/dot-rm_dupesPE.Rd man/easyLoad_FUN.Rd man/easyLoad_IDRmerged.Rd man/easyLoad_bed.Rd man/easyLoad_broadPeak.Rd man/easyLoad_narrowPeak.Rd man/easyLoad_seacr.Rd man/expandCigar.Rd man/fetchBam.Rd man/findMaxPos.Rd man/fragLen_calcStranded.Rd man/fragLen_fromMacs2Xls.Rd man/getReadLength.Rd man/get_mapped_reads.Rd man/ggellipse.Rd man/harmonize_seqlengths.Rd man/make_clustering_matrix.Rd man/merge_clusters.Rd man/prepare_fetch_GRanges.Rd man/prepare_fetch_GRanges_names.Rd man/prepare_fetch_GRanges_width.Rd man/quantileGRangesWidth.Rd man/reorder_clusters_hclust.Rd man/reorder_clusters_manual.Rd man/reorder_clusters_stepdown.Rd man/reverse_clusters.Rd man/safeBrew.Rd man/seqsetvis-package.Rd man/set_list2memb.Rd man/shift_anchor.Rd man/split_cluster.Rd man/ssvAnnotateSubjectGRanges.Rd man/ssvConsensusIntervalSets.Rd man/ssvFactorizeMembTable.Rd man/ssvFeatureBars.Rd man/ssvFeatureBinaryHeatmap.Rd man/ssvFeatureEuler.Rd man/ssvFeaturePie.Rd man/ssvFeatureUpset.Rd man/ssvFeatureVenn.Rd man/ssvFetchBam.Rd man/ssvFetchBam.single.Rd man/ssvFetchBamPE.RNA.Rd man/ssvFetchBamPE.Rd man/ssvFetchBamPE.single.Rd man/ssvFetchBigwig.Rd man/ssvFetchBigwig.single.Rd man/ssvFetchGRanges.Rd man/ssvFetchSignal.Rd man/ssvMakeMembTable-methods.Rd man/ssvOverlapIntervalSets.Rd man/ssvSignalBandedQuantiles.Rd man/ssvSignalClustering.Rd man/ssvSignalHeatmap.ClusterBars.Rd man/ssvSignalHeatmap.Rd man/ssvSignalLineplot.Rd man/ssvSignalLineplotAgg.Rd man/ssvSignalScatterplot.Rd man/ssv_mclapply.Rd man/test_peaks.Rd man/viewGRangesWinSample_dt.Rd man/viewGRangesWinSummary_dt.Rd man/within_clust_sort.Rd tests/testthat.R tests/testthat/test_anchor.R tests/testthat/test_annotation.R tests/testthat/test_applySpine.R tests/testthat/test_bugfix_uinque_names_factor.R tests/testthat/test_centerAtMax.R tests/testthat/test_centerFixedSizeGRanges.R tests/testthat/test_cigar.R tests/testthat/test_easyLoad.R tests/testthat/test_fetchBam.R tests/testthat/test_fetchBw.R tests/testthat/test_fetchBw_dt.R tests/testthat/test_fetchGRanges.R tests/testthat/test_fetch_PE.R tests/testthat/test_fetch_PE_RNA.R tests/testthat/test_fetch_parallel.R tests/testthat/test_force_skip.R tests/testthat/test_normalization.R tests/testthat/test_overlapIntervalSets.R tests/testthat/test_plots_return_data.R tests/testthat/test_prepare_fetch_GRanges.R tests/testthat/test_return_unprocessed.R tests/testthat/test_safeBrew.R tests/testthat/test_setPlotMakeMT.R tests/testthat/test_splice_count.R tests/testthat/test_ssvFactorizeMembTable.R tests/testthat/test_ssvFeaturePlots_specific.R tests/testthat/test_ssvFeaturePlots_universal.R tests/testthat/test_ssvSignalClustering.R tests/testthat/test_ssvSignalPlots.R tests/testthat/test_strand_flipping.R tests/testthat/test_viewGrangesWin_sample_vs_summary.R tests/testthat/test_within_sort_clust.R vignettes/seqsetvis_fetchBams.Rmd vignettes/seqsetvis_overview.Rmd