Man pages for compbiomed/animalcules
Statistical microbiome analysis on metagenomics data

align_targetAlign microbiome reads to a set of reference libraries
alpha_div_boxplotAlpha diversity boxplot
alpha_div_testGet alpha diversity
animalcules_idAnimalcules ID
animalcules-packageanimalcules: Statistical microbiome analysis on metagenomics...
bam_reheader_RReplace the header from a .bam file
combined_headerCreate a combined .bam header
counts_to_logcpmCovert a counts table to a relative abundances table
counts_to_relabuCovert a counts table to a relative abundances table
demultiplexDemultiplexing sequencing reads
df_char_to_factorFactorize all categorical columns
differential_abundanceDifferential abundance analysis
dimred_pcaDimensionality reduction through PCA
dimred_pcoaDimensionality reduction through PCoA
diversitiesGet alpha diversity
diversities_helpGet alpha diversity
diversity_beta_boxplotBeta diversity boxplot
diversity_beta_heatmapBeta diversity heatmap
diversity_beta_testBeta diversity test (by default we use bray-curtis distance)
do_alpha_div_testAlpha diversity statistical test
download_refseqDownload RefSeq genome libraries
extractReadsHelper function for demultiplexing
filter_categorizeCategorize continuous variables
filter_summary_bottomData visualization by barplot
filter_summary_topData visualization by pie chart
filter_unmapped_readsFilter unmapped reads
find_biomarkerIdentify biomarkers
find_taxon_matFind the Taxonomy Information Matrix
find_taxonomyFind the taxonomy for unlimited tids
find_taxonomy_300Find the taxonomy for maximum 300 tids
gini_simpsonGet alpha diversity using gini
grep_tidGreps the tid from the given identifier string
inverse_simpsonGet alpha diversity using inverse simpson
is.categoricalCheck if object is categorical
is.integer0check if integer(0)
MAEHost/Microbiome Toy MultiAssayExperiment
mae_pick_organismsModify organisms of multi-assay experiment object
mae_pick_samplesModify samples of multi-assay experiment object
merge_bam_filesMerge multiple .bam files
mk_subread_indexMake a Subread index
pct2strConverts decimal percentage to string with specified digits
percentFormat decimals to percentages
read_pathoscope_dataReads the data from PathoScope reports and returns a list of...
relabu_barplotPlot bar plots of sample and group level relative abundance
relabu_boxplotPlot boxplots comparing different organism prevalence across...
relabu_heatmapPlot heatmap of sample level counts in logcpm
run_animalculesFind the taxonomy for maximum 300 tids
shannonGet alpha diversity using shannon
simpson_indexGet alpha diversity using simpson
upsample_countsUpsample a counts table to a higher taxon level
compbiomed/animalcules documentation built on Jan. 23, 2019, 10:07 a.m.