/usr/lib/R/site-library/phyloseq/INDEX is in r-bioc-phyloseq 1.22.3-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 | DPCoA Calculate Double Principle Coordinate Analysis
(DPCoA) using phylogenetic distance
UniFrac Calculate weighted or unweighted (Fast) UniFrac
distance for all sample pairs.
[,otu_table,ANY,ANY,ANY-method
Method extensions to extraction operator for
phyloseq objects.
access Universal slot accessor function for
phyloseq-class.
build_tax_table Build a 'tax_table' from a named
possibly-jagged list
data-GlobalPatterns (Data) Global patterns of 16S rRNA diversity at
a depth of millions of sequences per sample
(2011)
data-enterotype (Data) Enterotypes of the human gut microbiome
(2011)
data-esophagus (Data) Small example dataset from a human
esophageal community (2004)
data-soilrep (Data) Reproducibility of soil microbiome data
(2011)
dist-class An S4 placeholder for the 'dist' class.
distance Calculate distance, dissimilarity
distanceMethodList List of distance method keys supported in
'distance'
estimate_richness Summarize alpha diversity
export_env_file Export environment (ENV) file for UniFrac
Server.
export_mothur_dist Export a distance object as '.names' and
'.dist' files for mothur
filter_taxa Filter taxa based on across-sample OTU
abundance criteria
filterfun_sample A sample-wise filter function builder analogous
to 'filterfun'.
gapstat_ord Estimate the gap statistic on an ordination
result
genefilter_sample Filter OTUs with arbitrary function,
sample-wise.
get_sample Returns all abundance values for species 'i'.
get_taxa Returns all abundance values of sample 'i'.
get_taxa_unique Get a unique vector of the observed taxa at a
particular taxonomic rank
get_variable Get the values for a particular variable in
sample_data
getslots.phyloseq Return the non-empty slot names of a phyloseq
object.
import Universal import method (wrapper) for
phyloseq-package
import_RDP_cluster Import RDP cluster file and return otu_table
(abundance table).
import_RDP_otu Import new RDP OTU-table format
import_biom Import phyloseq data from biom-format file
import_env_file Read a UniFrac-formatted ENV file.
import_mothur General function for importing mothur data
files into phyloseq.
import_mothur_dist Import mothur-formatted distance file
import_pyrotagger_tab Imports a tab-delimited version of the
pyrotagger output file.
import_qiime Import function to read the now legacy-format
QIIME OTU table.
import_qiime_otu_tax Import now legacy-format QIIME OTU table as a
list of two matrices.
import_qiime_sample_data
Import just 'sample_data' file from QIIME
pipeline.
import_uparse Import UPARSE file format
import_usearch_uc Import usearch table format ('.uc') to OTU
table
make_network Make microbiome network (igraph)
merge_phyloseq Merge arguments into one phyloseq object.
merge_phyloseq_pair Merge pair of phyloseq component data objects
of the same class.
merge_samples Merge samples based on a sample variable or
factor.
merge_taxa Merge a subset of the species in 'x' into one
species/taxa/OTU.
microbio_me_qiime Import microbio.me/qiime (QIIME-DB) data
package
mt Multiple testing of taxa abundance according to
sample categories/classes
nodeplotblank Function to avoid plotting node labels
nodeplotboot Generates a function for labeling bootstrap
values on a phylogenetic tree.
nodeplotdefault Generates a default node-label function
nsamples Get the number of samples.
ntaxa Get the number of taxa/species.
ordinate Perform an ordination on phyloseq data
otu_table Build or access the otu_table.
otu_table-class The S4 class for storing taxa-abundance
information.
otu_table<- Assign a new OTU Table to 'x'
parse_taxonomy_default
Parse elements of a taxonomy vector
phy_tree Retrieve phylogenetic tree ('phylo'-class) from
object.
phy_tree<- Assign a (new) phylogenetic tree to 'x'
phylo-class An S4 placeholder of the main phylogenetic tree
class from the ape package.
phyloseq Build phyloseq-class objects from their
components.
phyloseq-class The main experiment-level class for phyloseq
data
phyloseq-deprecated Depcrecated functions in the phyloseq package.
phyloseq-package Handling and analysis of high-throughput
phylogenetic sequence data.
phyloseq_to_deseq2 Convert phyloseq data to DESeq2 dds object
phyloseq_to_metagenomeSeq
Convert phyloseq data to MetagenomeSeq
MRexperiment object
plot_bar A flexible, informative barplot phyloseq data
plot_clusgap Create a ggplot summary of gap statistic
results
plot_heatmap Create an ecologically-organized heatmap using
ggplot2 graphics
plot_net Microbiome Network Plot using ggplot2
plot_network Microbiome Network Plot using ggplot2
plot_ordination General ordination plotter based on ggplot2.
plot_phyloseq Generic plot defaults for phyloseq.
plot_richness Plot alpha diversity, flexibly with ggplot2
plot_scree General ordination eigenvalue plotter using
ggplot2.
plot_tree Plot a phylogenetic tree with optional
annotations
prune_samples Define a subset of samples to keep in a
phyloseq object.
prune_taxa Prune unwanted OTUs / taxa from a phylogenetic
object.
psmelt Melt phyloseq data object into large data.frame
rank_names Retrieve the names of the taxonomic ranks
rarefy_even_depth Resample an OTU table such that all samples
have the same library size.
read_tree Somewhat flexible tree-import function
read_tree_greengenes Read GreenGenes tree released in annotated
newick format
refseq Retrieve reference sequences
('XStringSet'-class) from object.
rm_outlierf Set to FALSE any outlier species greater than f
fractional abundance.
sample_data Build or access sample_data.
sample_data-class The S4 for storing sample variables.
sample_data<- Assign (new) sample_data to 'x'
sample_names Get sample names.
sample_names<- Replace OTU identifier names
sample_sums Returns the total number of individuals
observed from each sample.
sample_variables Get the sample variables present in sample_data
show,otu_table-method method extensions to show for phyloseq objects.
show_mothur_cutoffs Show cutoff values available in a mothur file.
subset_ord_plot Subset points from an ordination-derived ggplot
subset_samples Subset samples by sample_data expression
subset_taxa Subset species by taxonomic expression
t Transpose 'otu_table-class' or 'phyloseq-class'
tax_glom Agglomerate taxa of the same type.
tax_table Build or access the taxonomyTable.
tax_table<- Assign a (new) Taxonomy Table to 'x'
taxa_are_rows Access taxa_are_rows slot from otu_table
objects.
taxa_are_rows<- Manually change taxa_are_rows through
assignment.
taxa_names Get species / taxa names.
taxa_names<- Replace OTU identifier names
taxa_sums Returns the total number of individuals
observed from each species/taxa/OTU.
taxonomyTable-class An S4 class that holds taxonomic classification
data as a character matrix.
threshrank Thresholded rank transformation.
threshrankfun A closure version of the 'threshrank' function.
tip_glom Agglomerate closely-related taxa using
single-linkage clustering.
topf Make filter fun. that returns the top f
fraction of taxa in a sample.
topk Make filter fun. the most abundant 'k' taxa
topp Make filter fun. that returns the most abundant
'p' fraction of taxa
transform_sample_counts
Transform abundance data in an 'otu_table',
sample-by-sample.
tree_layout Returns a data table defining the line segments
of a phylogenetic tree.
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