qiimer: Work with QIIME Output Files in R

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Open QIIME output files in R, compute statistics, and create plots from the data.

Author
Kyle Bittinger <kylebittinger@gmail.com>
Date of publication
2015-12-28 00:01:50
Maintainer
Kyle Bittinger <kylebittinger@gmail.com>
License
GPL (>= 2)
Version
0.9.4
URLs

View on CRAN

Man pages

biom_raw_data
Extract raw data from a BIOM object.
biom_taxonomy
Extract taxonomy info from a biom object.
dist_get
Retrieve distances from a '"dist"' object.
dist_groups
Create a data frame of distances between groups of items.
dist_subset
Extract parts of a '"dist"' object.
make_otu_table
Create an OTU table.
otu_heatmap
Create a heatmap of OTU counts.
qiimer
qiimer: Read QIIME output files and create plots
rarefaction_stats
Compute summary statistics for collated alpha diversity...
read_blast_table
Parse tabular output from BLAST.
read_qiime_distmat
Read a QIIME distance matrix file.
read_qiime_mapping_file
Read a QIIME sample mapping file.
read_qiime_otu_mapping
Parse an OTU mapping file from QIIME.
read_qiime_otu_table
Parse a QIIME OTU table file in "calssic" format.
read_qiime_rarefaction
Read a collated alpha diversity table from QIIME.
relmbeta
Sample dataset from murine gut microbiome
relmbeta_alpha
Shannon diversity measurements from murine gut microbiome
relmbeta_assignments
Taxonomic assignments from murine gut microbiome
relmbeta_biom
BIOM format object from murine gut microbiome
relmbeta_counts
OTU counts from murine gut microbiome
relmbeta_dist
Unweighted UniFrac distances from murine gut microbiome
saturated_rainbow
Saturated rainbow palette.
simplify_assignments
Reformat taxonomic assignments for presentation.
split_assignments
Split taxonomic assignment strings
taxonomic_ranks
Standard taxonomic ranks.

Files in this package

qiimer
qiimer/inst
qiimer/inst/tests
qiimer/inst/tests/test_biom.R
qiimer/inst/tests/test_distance_matrix.R
qiimer/inst/tests/test_otu_mapping.R
qiimer/inst/tests/test_blast.R
qiimer/inst/tests/test_otu_table.R
qiimer/inst/tests/test_alpha_diversity.R
qiimer/inst/tests/test_sample_mapping.R
qiimer/inst/testdata
qiimer/inst/testdata/otu_table.txt
qiimer/inst/testdata/sample_map.txt
qiimer/inst/testdata/otu_table_dense.biom
qiimer/inst/testdata/distmat.txt
qiimer/inst/testdata/otu_table_sparse.biom
qiimer/inst/testdata/otu_mapping.txt
qiimer/inst/testdata/observed_species.txt
qiimer/inst/testdata/blast_table.txt
qiimer/tests
qiimer/tests/run-all.R
qiimer/NAMESPACE
qiimer/data
qiimer/data/relmbeta_alpha.rda
qiimer/data/relmbeta_counts.rda
qiimer/data/relmbeta_dist.rda
qiimer/data/relmbeta_assignments.rda
qiimer/data/relmbeta_biom.rda
qiimer/data/relmbeta.rda
qiimer/R
qiimer/R/distance_matrix.R
qiimer/R/biom.R
qiimer/R/otu_mapping.R
qiimer/R/blast.R
qiimer/R/sample_mapping.R
qiimer/R/qiimer.R
qiimer/R/alpha_diversity.R
qiimer/R/otu_table.R
qiimer/README.md
qiimer/MD5
qiimer/DESCRIPTION
qiimer/man
qiimer/man/relmbeta_alpha.Rd
qiimer/man/relmbeta.Rd
qiimer/man/taxonomic_ranks.Rd
qiimer/man/read_qiime_otu_mapping.Rd
qiimer/man/otu_heatmap.Rd
qiimer/man/split_assignments.Rd
qiimer/man/relmbeta_counts.Rd
qiimer/man/read_qiime_rarefaction.Rd
qiimer/man/read_blast_table.Rd
qiimer/man/relmbeta_assignments.Rd
qiimer/man/biom_raw_data.Rd
qiimer/man/read_qiime_mapping_file.Rd
qiimer/man/read_qiime_otu_table.Rd
qiimer/man/rarefaction_stats.Rd
qiimer/man/relmbeta_biom.Rd
qiimer/man/simplify_assignments.Rd
qiimer/man/dist_subset.Rd
qiimer/man/dist_get.Rd
qiimer/man/relmbeta_dist.Rd
qiimer/man/saturated_rainbow.Rd
qiimer/man/read_qiime_distmat.Rd
qiimer/man/make_otu_table.Rd
qiimer/man/dist_groups.Rd
qiimer/man/qiimer.Rd
qiimer/man/biom_taxonomy.Rd