Package: rbiom 3.1.0

Daniel P. Smith

rbiom: Integrated Analysis and Visualization of Microbiome Data

A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses.

Authors:Daniel P. Smith [aut, cre], Alkek Center for Metagenomics and Microbiome Research [cph, fnd]

rbiom_3.1.0.tar.gz
rbiom_3.1.0.zip(r-4.7)rbiom_3.1.0.zip(r-4.6)rbiom_3.1.0.zip(r-4.5)
rbiom_3.1.0.tgz(r-4.6-any)rbiom_3.1.0.tgz(r-4.5-any)
rbiom_3.1.0.tar.gz(r-4.7-any)rbiom_3.1.0.tar.gz(r-4.6-any)
rbiom_3.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rbiom/json (API)

# Install 'rbiom' in R:
install.packages('rbiom', repos = c('https://cmmr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cmmr/rbiom/issues

Pkgdown/docs site:https://cmmr.github.io

On CRAN:

Conda:

7.45 score 18 stars 1 packages 182 scripts 3.2k downloads 2 mentions 101 exports 75 dependencies

Last updated from:8a9bb35967. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK306
source / vignettesOK234
linux-release-x86_64OK263
macos-release-arm64OK159
macos-oldrel-arm64OK144
windows-develOK261
windows-releaseOK247
windows-oldrelOK216
wasm-releaseOK164

Exports:.%<>%%>%adiv_boxplotadiv_corrplotadiv_matrixadiv_statsadiv_tableadiv_vectoras_rbiombabiesbdiv_boxplotbdiv_clustersbdiv_corrplotbdiv_distmatbdiv_heatmapbdiv_matrixbdiv_ord_plotbdiv_ord_tablebdiv_statsbdiv_tablebdplybiom_inflatebiom_mergebiom_relativizebiom_rescaleblplyconvert_to_animalculesconvert_to_biomformatconvert_to_phyloseqconvert_to_SEconvert_to_TSEddplydistmat_ord_tabledistmat_statsgemsggsaveglimpsehmp50ldplyleft_joinlist_metricsllplymatch_metricmtx_percentmtx_rarefymtx_rescalemutaten_cpusna.omitplot_heatmappullrare_corrplotrare_multiplotrare_stackedrarefyrarefy_colsread_biomread_fastaread_treerelocaterenamerescale_colsrescale_rowssample_applysample_sumsselectsliceslice_headslice_maxslice_minslice_sampleslice_tailstats_boxplotstats_corrplotstats_tablesubset_taxasuggest_inflate_depthssuggest_rarefy_depthtaxa_applytaxa_boxplottaxa_clusterstaxa_corrplottaxa_heatmaptaxa_maptaxa_matrixtaxa_meanstaxa_stackedtaxa_statstaxa_sumstaxa_tabletree_subsetwrite_biomwrite_countswrite_fastawrite_metadatawrite_mothurwrite_qiime2write_taxonomywrite_treewrite_xlsx

Dependencies:apebeeswarmbitbit64cellrangerclicliprclustercommonmarkcpp11crayoncurldigestdplyrecodiveemmeansestimabilityfarverfillpatterngenericsggbeeswarmggnewscaleggplot2ggrepelggtextgluegridtextgtablehmsisobandjpegjsonlitelabelinglatticelifecyclelitedownmagrittrmarkdownMASSMatrixmgcvmvtnormnlmenumDerivpatchworkpermutepillarpkgconfigplyrpngprettyunitsprogressR6RColorBrewerRcppreadrreadxlrematchrlangS7scalesstringistringrtibbletidyselecttzdbutf8vctrsveganviporviridisLitevroomwithrxfunxml2

Readme and manuals

Help Manual

Help pageTopics
Visualize alpha diversity with boxplots.adiv_boxplot
Visualize alpha diversity with scatterplots and trendlines.adiv_corrplot
Test alpha diversity for associations with metadata.adiv_stats
Calculate the alpha diversity of each sample.adiv_matrix adiv_table adiv_vector
Convert a variety of data types to an rbiom object.as_rbiom
Convert an rbiom object to a base R list.as.list.rbiom
Convert an rbiom object to a simple count matrix.as.matrix.rbiom
Longitudinal Stool Samples from Infants (n = 2,684)babies
Visualize BIOM data with boxplots.bdiv_boxplot
Cluster samples by beta diversity k-means.bdiv_clusters
Visualize beta diversity with scatterplots and trendlines.bdiv_corrplot
Display beta diversities in an all vs all grid.bdiv_heatmap
Ordinate samples and taxa on a 2D plane based on beta diversity distances.bdiv_ord_plot
Calculate PCoA and other ordinations, including taxa biplots and statistics.bdiv_ord_table
Test beta diversity for associations with metadata.bdiv_stats
Distance / dissimilarity between samples.bdiv_distmat bdiv_matrix bdiv_table
Apply a function to each subset of an rbiom object.bdply blply
Inflate Relative Abundances to Integer Countsbiom_inflate
Combine several rbiom objects into one.biom_merge
Relativize Counts to Proportionsbiom_relativize
Rescale Counts to a Specific Rangebiom_rescale
Convert biom data to an external package classconvert_to convert_to_animalcules convert_to_biomformat convert_to_phyloseq convert_to_SE convert_to_TSE
Run ordinations on a distance matrix.distmat_ord_table
Run statistics on a distance matrix vs a categorical or numeric variable.distmat_stats
Export data to QIIME 2 or mothur.export write_mothur write_qiime2
Global Enteric Multicenter Study (n = 1,006)gems
Get a glimpse of your metadata.glimpse.rbiom
Human Microbiome Project - demo dataset (n = 50)hmp50
Deprecated matrix transformationsmatrix_ops mtx_percent mtx_rarefy mtx_rescale rarefy_cols rescale_cols rescale_rows
Create, modify, and delete metadata fields.modify_metadata mutate.rbiom rename.rbiom
Create a heatmap with tracks and dendrograms from any matrix.plot_heatmap
Map sample names to metadata field values.pull.rbiom
Visualize rarefaction curves with scatterplots and trendlines.rare_corrplot
Combines rare_corrplot and rare_stacked into a single figure.rare_multiplot
Visualize the number of observations per sample.rare_stacked
Rarefy Counts to a Constant Depthrarefy
Parse counts, metadata, taxonomy, and phylogeny from a BIOM file.read_biom
Parse a fasta file into a named character vector.read_fasta
Read a newick formatted phylogenetic tree.read_tree
Summarize the taxa observations in each sample.sample_apply sample_sums
Subset to a specific number of samples.slice.rbiom slice_head.rbiom slice_max.rbiom slice_metadata slice_min.rbiom slice_sample.rbiom slice_tail.rbiom
Visualize categorical metadata effects on numeric values.stats_boxplot
Visualize regression with scatterplots and trendlines.stats_corrplot
Run non-parametric statistics on a data.frame.stats_table
Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.na.omit.rbiom subset subset.rbiom subset_taxa [.rbiom
Suggest Inflation Depthssuggest_inflate_depths
Suggest Rarefaction Depthsuggest_rarefy_depth
Visualize BIOM data with boxplots.taxa_boxplot
Cluster samples by taxa abundances k-means.taxa_clusters
Visualize taxa abundance with scatterplots and trendlines.taxa_corrplot
Display taxa abundances as a heatmap.taxa_heatmap
Map OTUs names to taxa names at a given rank.taxa_map
Display taxa abundances as a stacked bar graph.taxa_stacked
Test taxa abundances for associations with metadata.taxa_stats
Get summary taxa abundances.taxa_apply taxa_means taxa_sums
Taxa abundances per sample.taxa_matrix taxa_table
Create a subtree by specifying tips to keep.tree_subset
Evaluate expressions on metadata.with with.rbiom within.rbiom
Save an rbiom object to a file.write_biom write_counts write_fasta write_metadata write_taxonomy write_tree write_xlsx