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qiimer

The qiimer package provides R functions to read QIIME output files and create figures.

Types of files covered:

  • "Classic" format OTU tables
  • Distance matrices
  • Metadata mapping files
  • OTU mapping files (OTU ID to sequence ID)
  • Rarefied alpha diversity tables

Also included: convenience functions for BLAST tables, distance matrix objects, and biom-format OTU tables imported via the biom library.

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Version

Install

install.packages('qiimer')

Monthly Downloads

14

Version

0.9.4

License

GPL (>= 2)

Maintainer

Kyle Bittinger

Last Published

December 27th, 2015

Functions in qiimer (0.9.4)

otu_heatmap

Create a heatmap of OTU counts.
read_qiime_distmat

Read a QIIME distance matrix file.
dist_subset

Extract parts of a `"dist"` object.
dist_groups

Create a data frame of distances between groups of items.
taxonomic_ranks

Standard taxonomic ranks.
read_qiime_rarefaction

Read a collated alpha diversity table from QIIME.
read_qiime_mapping_file

Read a QIIME sample mapping file.
dist_get

Retrieve distances from a `"dist"` object.
relmbeta_alpha

Shannon diversity measurements from murine gut microbiome
biom_raw_data

Extract raw data from a BIOM object.
read_qiime_otu_table

Parse a QIIME OTU table file in "calssic" format.
qiimer

qiimer: Read QIIME output files and create plots
relmbeta_assignments

Taxonomic assignments from murine gut microbiome
saturated_rainbow

Saturated rainbow palette.
relmbeta_counts

OTU counts from murine gut microbiome
simplify_assignments

Reformat taxonomic assignments for presentation.
biom_taxonomy

Extract taxonomy info from a biom object.
relmbeta_biom

BIOM format object from murine gut microbiome
relmbeta

Sample dataset from murine gut microbiome
read_blast_table

Parse tabular output from BLAST.
relmbeta_dist

Unweighted UniFrac distances from murine gut microbiome
rarefaction_stats

Compute summary statistics for collated alpha diversity tables.
read_qiime_otu_mapping

Parse an OTU mapping file from QIIME.
make_otu_table

Create an OTU table.
split_assignments

Split taxonomic assignment strings