API for orionzhou/rmaize
Common bioinformatic utilities
| Global functions | |
|---|---|
| .copyTwobitFile | Source code |
| .forge.AGAPSmask | Source code |
| .forge.AMBmask | Source code |
| .forge.RMmask | Source code |
| .forge.TRFmask | Source code |
| .forgeFastaRzFileFromFastaFiles | Source code |
| .forgeMasksFile | Source code |
| .forgeRdaSeqFile | Source code |
| .forgeRdsSeqFile | Source code |
| .forgeTwobitFileFromFastaFiles | Source code |
| .getMasksObjname | Source code |
| .ls.objects | Source code |
| .readSeedFile | Source code |
| .removeCommentLines | Source code |
| .replace_non_ACGTN_with_N | Source code |
| .saveObjectToRdaFile | Source code |
| .saveObjectToRdsFile | Source code |
| .sortUCSCTwobitFile | Source code |
| .subsetTwobitFile | Source code |
| BSgenomeDataPkgSeed | Source code |
| MaskedBSgenomeDataPkgSeed | Source code |
| Mode | Man page Source code |
| bed_merge | Source code |
| cluster_motifs | Source code |
| cmp_cnt1 | Source code |
| cmp_cnt_grid | Source code |
| cmp_proportion | Man page Source code |
| cmp_proportion1 | Man page Source code |
| color_palette_plot | Source code |
| complete_sample_list | Man page Source code |
| desc_stat | Man page Source code |
| downsample | Source code |
| extract_lib_stats | Source code |
| extract_read_stats | Source code |
| filter_expr | Source code |
| fit_split | Man page Source code |
| flattern_gcoord | Man page Source code |
| flattern_gcoord_prepare | Man page Source code |
| forgeMasksFiles | Source code |
| forgeSeqFiles | Source code |
| forgeSeqlengthsRdaFile | Source code |
| forgeSeqlengthsRdsFile | Source code |
| generate_sample_id | Man page Source code |
| genome_dir | Man page Source code |
| getSeqSrcpaths | Source code |
| getSeqlengths | Source code |
| get_density | Man page Source code |
| get_grid | Man page Source code |
| get_gt_panel | Source code |
| get_model | Man page Source code |
| get_sra_meta | Man page Source code |
| get_tuner | Man page Source code |
| go_enrich | Man page Source code |
| hc_order_row | Man page Source code |
| heatmap_hc | Man page Source code |
| hyper_enrich | Man page Source code |
| hyper_enrich_m | Man page Source code |
| idist | Man page Source code |
| intersect_basepair | Man page Source code |
| intersect_cds_sv | Man page Source code |
| intersect_count | Man page Source code |
| intersect_gene | Man page Source code |
| intersect_idx | Man page Source code |
| intersect_idx_maxovlp | Man page Source code |
| intersect_idx_t | Man page Source code |
| intersect_once | Man page Source code |
| intersect_s | Man page Source code |
| intersect_score | Man page Source code |
| lg | Man page |
| liftover | Man page Source code |
| load_fonts | Man page Source code |
| load_txdb | Man page Source code |
| load_txdbs | Source code |
| lsos | Man page Source code |
| makeS4FromList | Source code |
| make_tile | Man page Source code |
| map_signif | Source code |
| merge_reps | Man page |
| metric_balanced | Man page Source code |
| metrics6 | Man page |
| ml0 | Man page Source code |
| ml1 | Man page Source code |
| multi_pie | Source code |
| no_x_axis | Source code |
| no_y_axis | Source code |
| o_margin | Source code |
| otheme | Man page Source code |
| pal_10 | Man page Source code |
| pal_12 | Man page Source code |
| pal_13 | Man page Source code |
| pal_23 | Man page Source code |
| pal_23b | Man page Source code |
| pal_gradient | Man page Source code |
| pal_shapes | Man page Source code |
| pie1 | Source code |
| plot_ase | Man page |
| plot_combo | Source code |
| plot_genes | Source code |
| plot_genes0 | Source code |
| plot_hclust | Man page |
| plot_hist | Man page Source code |
| plot_kmer | Source code |
| plot_pca | Man page |
| plot_ril_genotype | Man page |
| plot_syn | Source code |
| plot_tsne | Man page |
| plot_umap | Man page |
| prepare_syn | Source code |
| read.dcf2 | Source code |
| read_chrom_size | Source code |
| read_genome_conf | Man page Source code |
| read_go | Man page Source code |
| read_gspread | Man page Source code |
| read_gspread_master | Man page Source code |
| read_gt_panels | Source code |
| read_loci | Source code |
| read_projects | Source code |
| read_regions | Man page Source code |
| read_sra_run | Man page Source code |
| read_symbol | Man page |
| read_syn | Man page Source code |
| read_tf | Man page Source code |
| read_tis_spec | Source code |
| read_xref | Source code |
| readcount_norm | Man page Source code |
| recipe_ml | Source code |
| rename_mtf | Source code |
| rnaseq_cpm | Man page Source code |
| rnaseq_cpm_raw | Man page Source code |
| rnaseq_mapping_stat | Man page Source code |
| rnaseq_sample_meta | Man page Source code |
| sd2 | Source code |
| set_bound | Man page Source code |
| sortC | Man page Source code |
| sra_fill_replicate | Man page Source code |
| sum_mapping_stat | Source code |
| sum_stat_tibble | Man page Source code |
| test_enrich | Man page Source code |
| ttest_signif | Source code |
| txdb_gene | Source code |
| v3_to_v4 | Man page Source code |
| wfl_fit | Source code |
| wfl_metric | Source code |
| wfl_pred | Source code |
