Files in jrboyd/ssvRecipes

Recipes using seqsetvis

R/function_fix_xlsx_dates.R R/function_truncate_peak_file.R R/functions_GR_ovlerlaps.R R/functions_RNAseq_counts.R R/functions_RNAseq_salmon.R R/functions_alignment_mismatch.R R/functions_bfcif.R R/functions_bigwig_correlation.R R/functions_bw_cluster_summary.R R/functions_clusterProfiler.R R/functions_corrDiff.R R/functions_fetchBamPE.R R/functions_file_helpers.R R/functions_hclust.R R/functions_heatmap_with_sideplots.R R/functions_load_STAR_RNA_counts.R R/functions_multimapping.R R/functions_my_files.R R/functions_plot_ideogram.R R/functions_sample.R R/functions_scRNA_fetch.R R/functions_scRNAseq.R R/functions_scatter_with_side_density.R R/functions_scatterplot_with_side_density.R R/functions_stranded_bamFetch.R R/functions_syncDims.R R/functions_timestamps.R R/functions_tracks.R dev_bam_alignment.R dev_ontology.R dev_viral_snapshots.R man/alignFasta.Rd man/annotate_gr.Rd man/annotate_gr_clusters.Rd man/bfcif.Rd man/cache_FUN.Rd man/cache_gz.Rd man/corr_fragLens.Rd man/corr_fragLens.single.Rd man/counts_from_bams.Rd man/dot-get_files.Rd man/fetch_bw_summary.Rd man/fix_xlsx_dates.Rd man/gene_name_hs2mm.Rd man/get_gg_xrange.Rd man/get_gg_yrange.Rd man/get_hclust_gls.Rd man/get_meta_dt.Rd man/get_my_files.Rd man/get_rna_dt.Rd man/ggheatmap.dendro.Rd man/gr_distance_overlap.Rd man/guess_lib_from_file.Rd man/h.cluster_data.Rd man/h.cluster_members.Rd man/h.final_plot.Rd man/h.plot_parts_grouped.Rd man/h.plot_parts_individual.Rd man/is_gz.Rd man/is_url.Rd man/kill_jids.Rd man/load_matrix_from_ReadsPerGene.out.tab.Rd man/make_cell_dt_from_list.Rd man/make_msigdb_TERM2GENE.Rd man/myFetchStrandedBam.Rd man/myPlotDiffClusters.Rd man/myStrandDiff.Rd man/my_clusterProfiler_GO.Rd man/my_clusterProfiler_KEGG.Rd man/my_clusterProfiler_MSigDB.Rd man/my_clusterProfiler_table.Rd man/parse_xls.Rd man/parse_xls_reads.Rd man/plot-methods.Rd man/plotHomerKnowResults.Rd man/plot_bam_mismatch_dt.Rd man/plot_hclust_heatmap.Rd man/plot_hclust_heatmap.assemble.Rd man/plot_scatter_side_density.Rd man/plot_scatter_side_density.assemble.Rd man/plot_scatter_side_density.xy.Rd man/read.table.fix_xlsx_dates.Rd man/reorderHeatmapClusters.Rd man/rnaseq_asses_strandedness.Rd man/running_jids.Rd man/salmon_index_transcriptome.Rd man/salmon_tx_quant.Rd man/sampleCap.Rd man/show-methods.Rd man/ssvFetchBam.scRNA.Rd man/ssvFetchBamPE.RNA.Rd man/ssvH2-class.Rd man/ssvHeatmap2.Rd man/ssvR_plot_bam_mismatch.Rd man/ssvR_plot_ideogogram.Rd man/ssvR_plot_ideogogram_data.Rd man/star_align_fastq_PE.Rd man/star_align_fastq_SE.Rd man/star_align_fastq_core.Rd man/symbol2uniprot.Rd man/sync_height.Rd man/sync_width.Rd man/timestamp.mdy.Rd man/track_assembly.Rd man/track_chip.Rd man/track_ref.Rd man/track_rna.Rd man/truncate_peak_file.Rd man/wait_jids.Rd man/watch_jids.Rd man/writeBigBed.Rd man/writeFastaFromGR.Rd man/writeFastaFromSeq.Rd man/write_geneList_matrix.Rd vignettes/demo_heatmap_with_sideplots.Rmd vignettes/rnaseq_analysis.Rmd