Man pages for mworkentine/mattsUtils
Personal Utility Functions For Various Analysis
| add_taxonomy_column | Add taxonomy label |
| cluster_order | Cluster Order |
| cnetggplot | cnetggplot |
| compute_spia | compute spia with provided gene list does the bulk of the... |
| get_monophyletic_subsets | Get monophyletic subsets |
| get_richness | Get a dataframe with richness estimates |
| get_seq_stats | Sequence stats |
| get_sig_taxa | Get a list of significant taxa from a DESeq analysis |
| ggheatmap | Make a ggplot heatmap |
| lfc_plot | Log fold-change plot |
| make_heatmap | Make Heatmap |
| make_ordination_plots | Make ordination plots |
| make_prev_df | Make a prevalance dataframe |
| make_taxa_colours | Make colour palettes for taxa |
| mattsUtils | mattsUtils: Convience functions and utilies to help with my... |
| plot_bar2 | Plot bar 2 |
| plot_diagnositics | Diagnostic plots for a DESeq differential expression analysis |
| plot_featureCount_stats | Plot stats from featureCounts output |
| plot_genus_by_phylum | Plot genus by phylum |
| plot_num_seqs | Plot number of sequences |
| plot_OTUs | Plot OTUs |
| plotPCA2 | Plot PCA (modified) |
| prev_filt | Prevalance filter |
| prev_plot | Prevelance Plot |
| print_table | Print table |
| psmelt_dplyr | A dplyr version of psmelt |
| replace_counts | Replace counts |
| rlog_norm_otus | rlog normalize an OTU table |
| run_spia | Prepare gene lists and run spia |
| single_gene_plot | Single Gene Plot |
| subset_samples_safe | Subset samples 2 |
| subset_taxa_safe | Subset taxa 2 |
| summarize_taxonomy | Summarize taxonomy |
| tidy_phyloseq | Tidy phyloseq |
| upload_and_share | Upload and share |
| veganotu | Convert phyloseq otu table to vegan otu table |
| vst_transform | VST Tranform a phyloseq object |
