Man pages for bryancquach/omixjutsu
Utilities for omics analysis tasks
| assoc_matrix | Association matrix |
| below_max_cutoff | Detect samples below a specified cutoff value |
| beta_to_mvalue | DNA methylation M-values |
| cooks_outlier_pval_histogram | P-value histogram for outlier features |
| counts.DGEList | Get counts from DGEList object |
| exceeds_min_cutoff | Detect samples above a specified cutoff value |
| filter_dds_features | Filter lowly expressed features from a DESeq2DataSet... |
| filter_table | Exclude table dimenions by matching values. |
| get_cooks_cutoff | Get Cook's distance cutoff |
| get_cooks_outliers | Flag outliers using Cook's distance |
| get_design_mat | Create design matrix |
| get_gencode_chr_y_gene_ids | Retrieve protein-coding chrY gene IDs |
| get_gencode_mitochondrial_ids | Retrieve mitochondrial feature IDs |
| get_gencode_rrna_ids | Retrieve ribosomal RNA feature IDs |
| get_matrix_r2 | Calculate (adjusted) r-squared for a matrix |
| get_residual_matrix | Calculate residual matrix |
| ggpca | ggplot2-based PCA plot |
| ggscatter | ggplot2-based scatterplot |
| grouped_barplot | Grouped barplot |
| hist_boxplot | Histogram and jittered boxplot |
| hist_boxplot2 | Histogram and jittered boxplots partitioned by categories |
| ihw_diagnostic_plots | IHW diagnostic plots |
| ihw_partitioned_pval_weights | Stratified IHW p-value weights |
| ihw_pval_cdf | Stratified p-value eCDFs |
| ihw_pval_comparison | Compare p-value transformations |
| ihw_pval_decision_boundary | Plot IHW weight decision boundaries |
| ihw_pval_ridges | Stratified p-value density distributions |
| ihw_pval_scatter | Plot p-value vs. IHW variable ranking |
| ihw_stratified_pval_hist | Stratified p-value histograms |
| load_paired_end_qc_data | Load QC metrics data from paired-end RNA-seq processing |
| low_expression_filter | Filter lowly expressed features prior to DGE analysis |
| make_gencode_gene_id_map | Create GENCODE ID to gene name mapping |
| ma_plot | Bland-Altman plot |
| matrix_heatmap | Heatmap grid |
| merge_txi | Merge tximport objects |
| mvalue_to_beta | DNA methylation beta values |
| parse_by_trim_status | Partition rows by trimming status. |
| per_sample_count_distribution | Plot per sample count distribution |
| plot_adapter_content | Adapter content distribution line plot |
| plot_cooks_per_sample | Plot Cook's distance distributions per sample. |
| plot_cooks_vs_wald | Compare Cook's distances to Wald statistic ranks |
| plot_decoy_mapping_rate | Plot Salmon percent decoy fragments |
| plot_dna_contamination_ratio | Plot DNA contamination ratio |
| plot_dovetail_mapping_rate | Plot Salmon percent dovetail fragments |
| plot_expression_fraction | Plot feature set expression fraction |
| plot_failed_mapping_count | Plot Salmon failed mapping count |
| plot_frag_length | Fragment length frequency line plot |
| plot_gc_content | GC content distribution line plot |
| plot_gc_content_hist | GC content histogram |
| plot_gc_mean | Plot per sample mean read GC content |
| plot_gene_mapping_rate | Plot gene mapping rate |
| plot_hisat2_mapped_reads | Plot HISAT2 mapped read count |
| plot_hisat2_mapping_rate | Plot HISAT2 mapping percentage |
| plot_hisat2_stats | Plot HISAT2 mapping statistics as a scatterplot |
| plot_hisat2_vs_salmon | Plot HISAT2 vs. Salmon mapping rates |
| plot_inner_dist | Read pair inner distance distribution |
| plot_intergenic_genic_ratio | Plot intergenic-genic ratio |
| plot_junction_saturation | Splice junction saturation plot |
| plot_mapping_categories | Plot annotation category percentages for alignments |
| plot_partitioned_mean_expression | Plot partitioned mean expression |
| plot_partitioned_pc | Plot partitioned principal component |
| plot_pca | ggplot2-based PCA plot |
| plot_phred_mean | Plot per sample mean of per read mean PHRED scores |
| plot_phred_per_bp | Per base pair PHRED score plot |
| plot_phred_per_read | Per read PHRED frequency plot |
| plot_r2 | Plot (adjusted) r-squared for multiple models |
| plot_rin | Plot RIN scores |
| plot_salmon_categories | Plot Salmon mapping category percentages |
| plot_salmon_mapped_reads | Plot Salmon mapped read count |
| plot_salmon_mapping_pct | Plot Salmon mapping percentage |
| plot_salmon_score_filtered_rate | Plot Salmon percent score filtered fragments |
| plot_salmon_stats | Plot Salmon mapping statistics as a scatterplot |
| plot_seq_depth | Sequencing depth per sample scatterplot |
| plot_seq_depth_hist | Sequencing depth histogram |
| plot_seq_depth_vs_lib_complexity | Sequencing depth vs. library complexity scatterplot |
| plot_seq_duplication | Sequence duplication line plot |
| plot_shannon_index | Plot shannon diversity index |
| plot_trimmomatic_paired | Trimmomatic statistics histograms |
| plot_unique_read_pct | Unique read percentage per sample scatterplot |
| pval_histogram | Plot p-value histogram |
| pval_qqplot | Quantile-quantile plot |
| rint | Rank inverse-normal transform |
| select_replicates | Choose best replicates to keep |
| subset_gencode_gtf | Subset GENCODE GTF to specific features |
| subset_txi | Subsets the tables of a tximport object |
| volcano_plot | Volcano plot |
