Man pages for cb-42/cbmbtools
R Functions for Facilitating Microbiome Analyses
| agg_otus | Aggregate OTU data by another taxonomic level. |
| cbmbtools | cbmbtools: General purpose package containing functions and... |
| chunkify | Generate R Markdown code chunks. |
| export_norm_tax | Write metadata and normalized OTU data (trimmed) to a file.... |
| join_tax | Join a dataframe with a taxonomy table. |
| list_paired_fastq | Generate a list of paired fastq files from given directory. |
| load_shared | Reads in a file containing OTU count data and keeps OTUs... |
| load_tax | Reads in a file containing taxonomy data and performs basic... |
| make_hel_pca | Create hellinger transformed data and PCA model from... |
| many_rf | Generate a list of randomForest models. |
| paste_tax | Paste Genus information onto a vector of OTU numbers. |
| plot_many_rf_varimp | Using a list of random forest models, create ordered boxplots... |
| plot_ra | Create an ordered relative abundance plot |
| plot_spider | Create an ordination with spiders based on 'spider_vec' and... |
| rank_tax | Generate a ranked vector of OTUs or other taxonomic level. |
| taxon_sort_gather | Transform data from wide to long, join a taxonomic level,... |
| tsg_ind | Transform data from wide to long, without aggregating... |
