Man pages for g-antonello/gautils
An R package for quick microbiome data wrangle and visualization
| add_N_to_catVar | Add sample size to the value |
| add_percent_columns | Add percentages to multicolumn tables |
| adonis_to_table | Quick wrapper to format PERMANOVA results |
| bin_integer_into_integer | Bin an integer/numeric variable |
| clone_dir_structure | Clone directory structure (Not working yet) |
| corncob_results_into_list | Extract corncob results |
| date_to_Season | From date to its season |
| declutter.envir | Delete temporary or test objects in 'ls()' |
| deseq_results_into_list | From DESeq2 results to a list of data.frames |
| format_pval2 | Format P-values for tables |
| get_GEMMA_results | Get Gemma heritability results |
| get_SOLAR_results | Get SOLAR results |
| hello | Hello, World! |
| is.nucleotide | Is a sequence made of nucleotides? |
| metaphlan_to_phyloseq | Create a phyloseq object from Metaphlan profiles |
| open_target_directory | Open file/plot directory |
| phy_add_metadata_variables | Add metadata variables to a phyloseq |
| phy_alpha_div_into_phy_metadata | Add alpha diversities into phyloseq metadata |
| phy_barplotTaxa | Barplot taxa (beta) |
| phy_BasicStats | Basic Phyloseq stats |
| phy_beta_div_betw_withn | Beta diversity into group boxplots |
| phy_betaPlot | Easy and Nice MDS Plots |
| phy_betaPlotTaxon | Fancy MDS Plots |
| phy_drop_NA_vars | Drop NAs from selected variables |
| phy_heatmap | Heatmap of microbiota features, NOT EXPORTED, because I... |
| phyloseq_to_fasta | Save Refseqs of phyloseq into a .fasta |
| phyloseq_to_picrust2 | Phyloseq to Picrust input tables |
| phy_OtuMetaTable | merge otu and metadata table |
| phy_plotTaxon_boxplot | Boxplot of a taxon |
| phy_plotTaxon_hist | Quick histogram of taxa |
| phy_plotTaxon_scatter | Scatterplot of a taxon |
| phy_pruneTaxa | Remove taxa that have counts summing to n |
| phy_substitute_metadata | Substitute a phyloseq metadata with a new data.frame |
| phy_summarise_taxa_by_metadata | Summarise taxa by metadata |
| phy_tax_glom | Agglomerate at higher taxonomic rank/level |
| phy_transform | Transform microbiota counts |
| qklook | Glimpse into a table-like object A simple function to make a... |
| read_metaml_results_binary | Read MetaML binary classification output |
| samp_cond_means_sd | Create Sample conditional means and standard deviation |
| samp_cond_medians_iqr | Create Sample conditional means and standard deviation |
| show_palette_colors | View the colors of a HTML list |
| SOLAR_results_kbl | Show clean SOLAR results |
| table1.pvalues | calculate p-values in table1 objects |
