Man pages for cb-42/cbmbtools
R Functions for Facilitating Microbiome Analyses

agg_otusAggregate OTU data by another taxonomic level.
cbmbtoolscbmbtools: General purpose package containing functions and...
chunkifyGenerate R Markdown code chunks.
export_norm_taxWrite metadata and normalized OTU data (trimmed) to a file....
join_taxJoin a dataframe with a taxonomy table.
list_paired_fastqGenerate a list of paired fastq files from given directory.
load_sharedReads in a file containing OTU count data and keeps OTUs...
load_taxReads in a file containing taxonomy data and performs basic...
make_hel_pcaCreate hellinger transformed data and PCA model from...
many_rfGenerate a list of randomForest models.
paste_taxPaste Genus information onto a vector of OTU numbers.
plot_many_rf_varimpUsing a list of random forest models, create ordered boxplots...
plot_raCreate an ordered relative abundance plot
plot_spiderCreate an ordination with spiders based on 'spider_vec' and...
rank_taxGenerate a ranked vector of OTUs or other taxonomic level.
taxon_sort_gatherTransform data from wide to long, join a taxonomic level,...
tsg_indTransform data from wide to long, without aggregating...
cb-42/cbmbtools documentation built on Jan. 9, 2021, 1:38 a.m.