Man pages for lefeverde/basicOmics
Package for basic statistical tests on Omics data
| basic_linear_regression | Function performs lm over accross a number of genes |
| basic_logistic_regression | Performs logistic regression with numerous Y vals |
| better_model_matrix | Creates a much nicer formatted design matrix than the default... |
| create_test_dds | Title |
| dge_wrapper | Wrapper function to create dge from txi |
| enrich_go_wrapper | Performs enrichment analysis accross all GO domains |
| enrich_pathway_wrapper | Performs enrichment analysis using KEGG, REACTOME, DO, and... |
| enrich_wrapper | Over Representation analysis (ORA) |
| ensembl_to_entrez_genes | Converts ensembl to entrez |
| expression_summaries | Returns summaries of gene expression |
| gene_quantile_filter | Gene expression filter by quantile |
| get_deseq2_results | Returns DESeq2 results in long format |
| get_geneSets | Extract genes sets from a pathway results data.frame |
| get_lfc | Gets lfc from a pathway res df |
| get_limma_results | get results from limma fit object |
| get_overlap_matix | Creates matrix of overlap ratios |
| increase_xy_lims | Returns expanded coordinates of a ggplot |
| lmlist_to_df | Turn summary object from lm into a data.frame |
| make_pca_plot_data | Title |
| pca_categorical_triplot | PCA categorical triplot |
| pca_data_wrapper | Title |
| pca_plotter | Plots PC1 by PC2 using ggplot |
| select_genes_by_variance | Selects the top n genes by variance |
| split_by_reg | Split a named vector of DEGs by fold change |
| split_fix_names | Split names by delim character |
| uniquefy_base | Base function which does the uniquefying |
| uniquefy_by_abs_max | Return a unique data.frame by max value |
| uniquefy_by_variance | Uniquefy by variance |
| venn_maker | Venn maker |
| volcano_plotter | Creates a volcano plot using data in long format |
| voom_sva_wrapper | Runs voom to sva pipeline |
| wilcoxOrKruskalOnA | Comparison of distributions of sample groups |
