Man pages for jrboyd/ssvRecipes
Recipes using seqsetvis
| alignFasta | calls STAR on fasta |
| annotate_gr | my_annotate |
| annotate_gr_clusters | annotate_gr_clusters |
| bfcif | bfcif |
| cache_FUN | Title |
| cache_gz | cache_gz |
| corr_fragLens | compares correlation of specified fragLens to un-extended... |
| corr_fragLens.single | returns correlation scores for all regions in qgr as... |
| counts_from_bams | Title |
| dot-get_files | Title |
| fetch_bw_summary | Title |
| fix_xlsx_dates | fix_xlsx_dates |
| gene_name_hs2mm | gene_name_gs2mm |
| get_gg_xrange | returns x limits of a ggplot |
| get_gg_yrange | returns y limits of a ggplot |
| get_hclust_gls | get_hclust_gls |
| get_meta_dt | get_meta_dt |
| get_my_files | returns files from a root directory stored in sub directories... |
| get_rna_dt | get_rna_dt |
| ggheatmap.dendro | Title |
| gr_distance_overlap | gr_distance |
| guess_lib_from_file | guess_lib_from_file |
| h.cluster_data | clust data.table accessor |
| h.cluster_members | cluster members accessor |
| h.final_plot | final_plot accessor |
| h.plot_parts_grouped | h.plot_parts_grouped |
| h.plot_parts_individual | h.plot_parts_individual |
| is_gz | Title |
| is_url | is_url |
| kill_jids | Title |
| load_matrix_from_ReadsPerGene.out.tab | load_matrix_from_ReadsPerGene.out.tab |
| make_cell_dt_from_list | Title |
| make_msigdb_TERM2GENE | make_msigdb_TERM2GENE |
| my_clusterProfiler_GO | my_clusterProfiler_fromGenes |
| my_clusterProfiler_KEGG | my_clusterProfiler_KEGG |
| my_clusterProfiler_MSigDB | my_clusterProfiler_MSigDB |
| my_clusterProfiler_table | clusterProfiler_table |
| myFetchStrandedBam | myFetchStrandedBam |
| myPlotDiffClusters | different plots for showing strand differences |
| myStrandDiff | subtracts minus from plus strand |
| parse_xls | parse lines in xls |
| parse_xls_reads | parse lines in xls for treatment and control |
| plot_bam_mismatch_dt | Title |
| plot_hclust_heatmap | Title |
| plot_hclust_heatmap.assemble | Title |
| plotHomerKnowResults | Plots knowresults from homer results directory |
| plot-methods | plot method for ssvH2 |
| plot_scatter_side_density | Title |
| plot_scatter_side_density.assemble | synchronizes margins of central scatterplot to align density... |
| plot_scatter_side_density.xy | plot a scatterplot with sets in color |
| read.table.fix_xlsx_dates | read.table.fix_xlsx_dates |
| reorderHeatmapClusters | manually reorder ssvHeatmap2 clusters works with any tidy... |
| rnaseq_asses_strandedness | rnaseq_asses_strandedness |
| running_jids | Title |
| salmon_index_transcriptome | salmon_index_transcriptome |
| salmon_tx_quant | Title |
| sampleCap | Title |
| show-methods | print method for ssvH2 |
| ssvFetchBamPE.RNA | ssvFetchBamPE |
| ssvFetchBam.scRNA | Title |
| ssvH2-class | ssvH2 |
| ssvHeatmap2 | seqsetvis improved Heatmap |
| ssvR_plot_bam_mismatch | ssvR_plot_bam_mismatch |
| ssvR_plot_ideogogram | ssvR_plot_ideogogram |
| ssvR_plot_ideogogram_data | ssvR_plot_ideogogram_data |
| star_align_fastq_core | Title |
| star_align_fastq_PE | Title |
| star_align_fastq_SE | Title |
| symbol2uniprot | symbol2uniprot |
| sync_height | sync ggplot heights |
| sync_width | sync ggplot widths |
| timestamp.mdy | timestamp.mdy |
| track_assembly | Title |
| track_chip | track_chip |
| track_ref | track_ref |
| track_rna | track_rna |
| truncate_peak_file | truncate_peak_file |
| wait_jids | Title |
| watch_jids | Title |
| writeBigBed | Write gr to bigbed file |
| writeFastaFromGR | write a fasta file of specified read_size from reference... |
| writeFastaFromSeq | write a fasta file of specified read_size from reference... |
| write_geneList_matrix | write_geneList_matrix |
