Files in bryancquach/omixjutsu

Utilities for omics analysis tasks

R/deseq2.R R/dge_utils.R R/gencode_utils.R R/ihw.R R/limma.R R/model_selection.R R/plot_utils.R R/rnaseq_workflow_qc.R R/table_utils.R R/transformations.R README.md man/assoc_matrix.Rd man/below_max_cutoff.Rd man/beta_to_mvalue.Rd man/cooks_outlier_pval_histogram.Rd man/counts.DGEList.Rd man/exceeds_min_cutoff.Rd man/filter_dds_features.Rd man/filter_table.Rd man/get_cooks_cutoff.Rd man/get_cooks_outliers.Rd man/get_design_mat.Rd man/get_gencode_chr_y_gene_ids.Rd man/get_gencode_mitochondrial_ids.Rd man/get_gencode_rrna_ids.Rd man/get_matrix_r2.Rd man/get_residual_matrix.Rd man/ggpca.Rd man/ggscatter.Rd man/grouped_barplot.Rd man/hist_boxplot.Rd man/hist_boxplot2.Rd man/ihw_diagnostic_plots.Rd man/ihw_partitioned_pval_weights.Rd man/ihw_pval_cdf.Rd man/ihw_pval_comparison.Rd man/ihw_pval_decision_boundary.Rd man/ihw_pval_ridges.Rd man/ihw_pval_scatter.Rd man/ihw_stratified_pval_hist.Rd man/load_paired_end_qc_data.Rd man/low_expression_filter.Rd man/ma_plot.Rd man/make_gencode_gene_id_map.Rd man/matrix_heatmap.Rd man/merge_txi.Rd man/mvalue_to_beta.Rd man/parse_by_trim_status.Rd man/per_sample_count_distribution.Rd man/plot_adapter_content.Rd man/plot_cooks_per_sample.Rd man/plot_cooks_vs_wald.Rd man/plot_decoy_mapping_rate.Rd man/plot_dna_contamination_ratio.Rd man/plot_dovetail_mapping_rate.Rd man/plot_expression_fraction.Rd man/plot_failed_mapping_count.Rd man/plot_frag_length.Rd man/plot_gc_content.Rd man/plot_gc_content_hist.Rd man/plot_gc_mean.Rd man/plot_gene_mapping_rate.Rd man/plot_hisat2_mapped_reads.Rd man/plot_hisat2_mapping_rate.Rd man/plot_hisat2_stats.Rd man/plot_hisat2_vs_salmon.Rd man/plot_inner_dist.Rd man/plot_intergenic_genic_ratio.Rd man/plot_junction_saturation.Rd man/plot_mapping_categories.Rd man/plot_partitioned_mean_expression.Rd man/plot_partitioned_pc.Rd man/plot_pca.Rd man/plot_phred_mean.Rd man/plot_phred_per_bp.Rd man/plot_phred_per_read.Rd man/plot_r2.Rd man/plot_rin.Rd man/plot_salmon_categories.Rd man/plot_salmon_mapped_reads.Rd man/plot_salmon_mapping_pct.Rd man/plot_salmon_score_filtered_rate.Rd man/plot_salmon_stats.Rd man/plot_seq_depth.Rd man/plot_seq_depth_hist.Rd man/plot_seq_depth_vs_lib_complexity.Rd man/plot_seq_duplication.Rd man/plot_shannon_index.Rd man/plot_trimmomatic_paired.Rd man/plot_unique_read_pct.Rd man/pval_histogram.Rd man/pval_qqplot.Rd man/rint.Rd man/select_replicates.Rd man/subset_gencode_gtf.Rd man/subset_txi.Rd man/volcano_plot.Rd tests/code_linting/r/lintr/lint.R