Files in joey711/phyloseq
Handling and analysis of high-throughput microbiome census data
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/IO-methods.R
R/allClasses.R
R/allData.R
R/allPackage.R
R/almostAllAccessors.R
R/as-methods.R
R/assignment-methods.R
R/deprecated_functions.R
R/distance-methods.R
R/extend_DESeq2.R
R/extend_metagenomeSeq.R
R/extend_vegan.R
R/extract-methods.R
R/merge-methods.R
R/multtest-wrapper.R
R/network-methods.R
R/ordination-methods.R
R/otuTable-class.R
R/phylo-class.R
R/phyloseq-class.R
R/plot-methods.R
R/sampleData-class.R
R/show-methods.R
R/taxonomyTable-class.R
R/transform_filter-methods.R
R/validity-methods.R
README.html
README.md
TODO.txt
data/GlobalPatterns.RData
data/datalist
data/enterotype.RData
data/esophagus.RData
data/soilrep.RData
inst/CITATION
inst/NEWS
inst/doc/Unweighted_UniFrac.RData
inst/extdata/GP_otu_table_rand_short.txt.gz
inst/extdata/GP_tree_rand_short.newick.gz
inst/extdata/biom-refseq.fasta
inst/extdata/biom-tree.phy
inst/extdata/esophagus.fn.list.gz
inst/extdata/esophagus.fn.shared.gz
inst/extdata/esophagus.good.groups.gz
inst/extdata/esophagus.tree.gz
inst/extdata/gg13-5-73.tree.gz
inst/extdata/gp500-pycogent.py
inst/extdata/gp500-uuf.csv
inst/extdata/gp500-wuf.csv
inst/extdata/gp500-wufu.csv
inst/extdata/gp500test.env.txt
inst/extdata/gp500test.tree
inst/extdata/master_map.txt
inst/extdata/min_dense_otu_table.biom
inst/extdata/min_sparse_otu_table.biom
inst/extdata/mothur_example.cons.taxonomy.gz
inst/extdata/phyloseq.png
inst/extdata/qiime500-refseq.fasta
inst/extdata/rformat_dist_0.03.txt.gz
inst/extdata/rich_dense_otu_table.biom
inst/extdata/rich_sparse_otu_table.biom
inst/extdata/study_1457_split_library_seqs_and_mapping.zip
inst/extdata/study_816_split_library_seqs_and_mapping.tar.gz
inst/extdata/study_816_split_library_seqs_and_mapping.zip
inst/extdata/study_gp.txt
inst/extdata/usearch.uc
inst/scripts/installer.R
man/DPCoA.Rd
man/JSD.Rd
man/UniFrac-methods.Rd
man/access.Rd
man/assign-otu_table.Rd
man/assign-phy_tree.Rd
man/assign-sample_data.Rd
man/assign-sample_names.Rd
man/assign-tax_table.Rd
man/assign-taxa_are_rows.Rd
man/assign-taxa_names.Rd
man/build_tax_table.Rd
man/capscale-phyloseq-methods.Rd
man/cca-rda-phyloseq-methods.Rd
man/chunkReOrder.Rd
man/data-GlobalPatterns.Rd
man/data-enterotype.Rd
man/data-esophagus.Rd
man/data-soilrep.Rd
man/decorana.Rd
man/dist-class.Rd
man/distance.Rd
man/distanceMethodList.Rd
man/envHash2otu_table.Rd
man/estimate_richness.Rd
man/export_env_file.Rd
man/export_mothur_dist.Rd
man/extract-methods.Rd
man/filter_taxa.Rd
man/filterfun_sample.Rd
man/fix_phylo.Rd
man/gapstat_ord.Rd
man/genefilter_sample-methods.Rd
man/get.component.classes.Rd
man/get_sample-methods.Rd
man/get_taxa-methods.Rd
man/get_taxa_unique.Rd
man/get_variable.Rd
man/getslots.phyloseq.Rd
man/import.Rd
man/import_RDP_cluster.Rd
man/import_RDP_otu.Rd
man/import_biom.Rd
man/import_env_file.Rd
man/import_mothur.Rd
man/import_mothur_constaxonomy.Rd
man/import_mothur_dist.Rd
man/import_mothur_groups.Rd
man/import_mothur_otu_table.Rd
man/import_mothur_otulist.Rd
man/import_mothur_shared.Rd
man/import_pyrotagger_tab.Rd
man/import_qiime.Rd
man/import_qiime_otu_tax.Rd
man/import_qiime_sample_data.Rd
man/import_uparse.Rd
man/import_usearch_uc.Rd
man/index_reorder.Rd
man/intersect_taxa.Rd
man/make_network.Rd
man/merge_phyloseq.Rd
man/merge_phyloseq_pair-methods.Rd
man/merge_samples-methods.Rd
man/merge_taxa-methods.Rd
man/metaMDS.Rd
man/microbio_me_qiime.Rd
man/mt-methods.Rd
man/nodeplotblank.Rd
man/nodeplotboot.Rd
man/nodeplotdefault.Rd
man/nsamples-methods.Rd
man/ntaxa-methods.Rd
man/ordinate.Rd
man/otu_table-class.Rd
man/otu_table-methods.Rd
man/parseTaxonomy-functions.Rd
man/pcoa.Rd
man/phy_tree-methods.Rd
man/phylo-class.Rd
man/phylo.Rd
man/phyloseq-class.Rd
man/phyloseq-deprecated.Rd
man/phyloseq-package.Rd
man/phyloseq.Rd
man/phyloseq_to_deseq2.Rd
man/phyloseq_to_metagenomeSeq.Rd
man/plot_bar.Rd
man/plot_clusgap.Rd
man/plot_heatmap.Rd
man/plot_net.Rd
man/plot_network.Rd
man/plot_ordination.Rd
man/plot_phyloseq-methods.Rd
man/plot_richness.Rd
man/plot_scree.Rd
man/plot_tree.Rd
man/prune_samples-methods.Rd
man/prune_taxa-methods.Rd
man/psmelt.Rd
man/rank_names.Rd
man/rarefy_even_depth.Rd
man/read_tree.Rd
man/read_tree_greengenes.Rd
man/reconcile_categories.Rd
man/refseq-methods.Rd
man/rm_outlierf.Rd
man/sample_data-class.Rd
man/sample_data-methods.Rd
man/sample_names-methods.Rd
man/sample_sums.Rd
man/sample_variables.Rd
man/show-methods.Rd
man/show_mothur_cutoffs.Rd
man/splat.phyloseq.objects.Rd
man/subset_ord_plot.Rd
man/subset_samples-methods.Rd
man/subset_taxa-methods.Rd
man/tax_glom.Rd
man/tax_table-methods.Rd
man/taxa_are_rows-methods.Rd
man/taxa_names-methods.Rd
man/taxa_sums.Rd
man/taxonomyTable-class.Rd
man/threshrank.Rd
man/threshrankfun.Rd
man/tip_glom.Rd
man/topf.Rd
man/topk.Rd
man/topp.Rd
man/transformcounts.Rd
man/transpose-methods.Rd
man/tree_layout.Rd
tests/testthat-phyloseq.R
tests/testthat/test-IO.R
tests/testthat/test-distance.R
tests/testthat/test-merge.R
tests/testthat/test-phyloseq.R
tests/testthat/test-plot.R
tests/testthat/test-rarefy.R
tests/testthat/test-subset.R
tests/testthat/test-transform.R
vignettes/import_qiime_directory_structure.jpg
vignettes/phyloseq-FAQ.Rmd
vignettes/phyloseq-analysis.Rmd
vignettes/phyloseq-basics.Rmd
vignettes/phyloseq-mixture-models.Rmd
vignettes/phyloseq_classes_7.png
