Man pages for kylebittinger/qiimer
Work with QIIME Output Files in R

biom_raw_dataExtract raw data from a BIOM object.
biom_taxonomyExtract taxonomy info from a biom object.
dist_getRetrieve distances from a '"dist"' object.
dist_groupsCreate a data frame of distances between groups of items.
dist_subsetExtract parts of a '"dist"' object.
make_otu_tableCreate an OTU table.
otu_heatmapCreate a heatmap of OTU counts.
qiimerqiimer: Read QIIME output files and create plots
rarefaction_statsCompute summary statistics for collated alpha diversity...
read_blast_tableParse tabular output from BLAST.
read_qiime_distmatRead a QIIME distance matrix file.
read_qiime_mapping_fileRead a QIIME sample mapping file.
read_qiime_otu_mappingParse an OTU mapping file from QIIME.
read_qiime_otu_tableParse a QIIME OTU table file in "calssic" format.
read_qiime_rarefactionRead a collated alpha diversity table from QIIME.
relmbetaSample dataset from murine gut microbiome
relmbeta_alphaShannon diversity measurements from murine gut microbiome
relmbeta_assignmentsTaxonomic assignments from murine gut microbiome
relmbeta_biomBIOM format object from murine gut microbiome
relmbeta_countsOTU counts from murine gut microbiome
relmbeta_distUnweighted UniFrac distances from murine gut microbiome
saturated_rainbowSaturated rainbow palette.
simplify_assignmentsReformat taxonomic assignments for presentation.
split_assignmentsSplit taxonomic assignment strings
taxonomic_ranksStandard taxonomic ranks.
kylebittinger/qiimer documentation built on May 21, 2017, 7:33 a.m.