Package: strainspy 0.99.2

strainspy: Strain Level Microbiome Wide Association Studies

Fits statistical models to detect microbial strains associated with a phenotype. For small sample sizes, models can be fitted using empirical Bayes maximum a posteriori (MAP) priors to improve detection power. Supports various experimental design scenarios, including repeated measures.

Authors:Gerry Tonkin-Hill [aut], Sudaraka Mallawarachchi [aut, cre]

strainspy_0.99.2.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
strainspy/json (API)

# Install 'strainspy' in R:

install.packages('strainspy', repos = c('https://sudaraka88.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gtonkinhill/strainspy/issues

On CRAN:

software microbiome metagenomics microbialstrain differentialexpression regression experimentaldesign sequencing

5.82 score 13 stars 46 scripts 40 exports 138 dependencies

Last updated from:efc140d91a. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	682
source / vignettes	OK	344
linux-release	NOTE	718
macos-release	NOTE	834
macos-oldrel	NOTE	676
windows-devel	NOTE	790
windows-release	NOTE	825
windows-oldrel	NOTE	708
wasm-release	OK	200

Exports:abundanceFit ani_distance caseControlFit comp_ani_diff_and_posthoc_test compute_eb_priors define_priors estimate_beta_diversity estimate_sample_richness extract_fixef_priors extract_strainspy filter_by_presence getContigNames getGenomes getResiduals getSamples getZICoefficients glmObFit glmQBFit glmZiBFit hadjust merge_metaphlan_files merge_sourmash_files merge_sylph_files modify_metadata plot_ani_dist plot_histogram plot_manhattan plot_mds plot_pca_biplot plot_prior_bootstrap plot_volcano prep_for_prediction read_metaphlan read_sourmash read_sylph read_taxonomy show strainspy summary top_hits

Dependencies:abind ape aplot backports base64enc BH Biobase BiocGenerics BiocParallel boot broom bslib cachem cli codetools colorspace cowplot cpp11 data.table DelayedArray Deriv digest doBy dplyr evaluate farver fastmap FMStable fontawesome fontBitstreamVera fontLiberation fontquiver forecast formatR fracdiff fs futile.logger futile.options gdtools generics GenomicRanges ggforce ggfun ggiraph ggplot2 ggplotify ggrepel ggthemes ggtree glmmTMB glue gridExtra gridGraphics gtable harmonicmeanp highr htmltools htmlwidgets IRanges isoband jquerylib jsonlite knitr labeling lambda.r lattice lazyeval lifecycle lme4 lmerTest lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minqa modelr nlme nloptr nnet numDeriv patchwork pbkrtest pillar pkgconfig polyclip purrr R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown S4Arrays S4Vectors S7 sandwich sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment systemfonts tibble tidyr tidyselect tidytree timeDate tinytex TMB treeio tweenr urca utf8 vctrs viridis viridisLite withr xfun XVector yaml yulab.utils zoo

strainspy Workflow

Rendered fromstrainspy-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-09-02
Started: 2026-09-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
abundanceFit	abundanceFit
ani_distance	ani_distance
caseControlFit	caseControlFit
Validate a 'progress' argument	check_progress
Stop if sample or feature names are not unique	check_unique_names
Automatically clean contig names for plots	clean_contig_names
Compute the mean ANI differences for contigs with an identity effect and perform posthoc testing to establish support for each hit.	comp_ani_diff_and_posthoc_test
Constructor for strainspy_priors using empirical Bayes estimation	compute_eb_priors
Constructor for strainspy_priors using preset or user defined priors	define_priors
Estimate beta diversity from ANI	estimate_beta_diversity
Estimate species richness and coverage of reference strains using ANI	estimate_sample_richness
Access fixef priors needed for ordinal beta regression	extract_fixef_priors extract_fixef_priors,strainspy_priors-method
Extract data from a StrainSpy 'SummarizedExperiment' object in long format	extract_strainspy
Identify per-feature model fits that failed	failed_fit_index
filter_by_presence	filter_by_presence
filter_by_presence_with_rescale_abundance	filter_by_presence_and_rescale
Filter strains based on subject and time aware manner - useful for longitudinal datasets	filter_by_presence_longitudinal
Fit a linear model for a Single Feature	fit_lm
Fit a linear model with random effects for a single feature	fit_lmer
Fit Logistic Regression for a Single Feature	fit_logit_model
Fit Ordinal Beta Regression for a Single Feature	fit_ob_model
Fit quasibinomial regression for a Single Feature	fit_qb_model
Fit Zero-Inflated Beta Regression for a Single Feature	fit_zero_inflated_beta
Fit Zero-Inflated Beta Regression for a Single Feature using the gamlss package	fit_zero_inflated_beta_gamlss
Generate colours for Manhattan plots	get_colors
Generate a confusion matrix for a fitted model	get_confusion_mx
Get Contig names in a fit object	getContigNames getContigNames,strainspy_fit-method
Get Genomes in a fit object	getGenomes getGenomes,strainspy_fit-method
Access Residuals	getResiduals getResiduals,strainspy_fit-method
Get Sample names in a fit object	getSamples getSamples,strainspy_fit-method
Access Zero-Inflation Coefficients	getZICoefficients getZICoefficients,strainspy_fit-method
glmObFit	glmObFit
glmQBFit TODO: Implement return of vcov info. Patched for compatibility (returns NULL)	glmQBFit
glmZiBFit	glmZiBFit
Performs hierarchical taxonomy aware adjustment of p-values.	hadjust
merge_metaphlan_files	merge_metaphlan_files
merge_sourmash_files	merge_sourmash_files
merge_sylph_files	merge_sylph_files
Add or modify metadata in a 'SummarizedExperiment' object	modify_metadata
Remove random effects from model	nobars_
Offset ANI by a fixed value	offset_ANI
Generate a violin or box plot for a subset of contigs for a categorical phenotype.	plot_ani_dist
Generate a histogram for a single contig for a categorical phenotype.	plot_histogram
Generate a strain Manhattan plot from a strainspy_fit object	plot_manhattan
Generate a Manhattan plot from a strainspy_fit object, with the option to add ground truth	plot_manhattan_gt
Generate a 'conventional' Manhattan plot for the strain all strains.	plot_manhattan_tree
Plot MDS of ANI data	plot_mds
plot_pca_biplot	plot_pca_biplot
Plot method for strainspy_priors objects	plot_prior_bootstrap plot_prior_bootstrap,strainspy_priors-method
Generate a Volcano Plot from a betaGLM Object	plot_volcano
Prepare a caret-compatible prediction data frame from a SummarizedExperiment	prep_for_prediction
read_metaphlan	read_metaphlan
read_sourmash	read_sourmash
Read Sylph query or profile output file and create a SummarizedExperiment object	read_sylph
Read and process a taxonomy file in Sylph format	read_taxonomy
Transform ANI Data to Simulate a Treatment Effect	rescale_beta
Resolve and construct priors for model fitting	resolve_priors
Show Method for strainspy_fit	show,strainspy_fit-method
Show method for strainspy_priors objects	show,strainspy_priors-method
Strainspy Wrapper	strainspy
strainspy_fit: A Class for storing fit data from all strainspy models	strainspy_fit-class
strainspy_priors: A Class for storing model fitting priors	strainspy_priors-class
Summary Method for strainspy_fit	summary,strainspy_fit-method
Provides the top results of a strainspy_fit object, sorted by adjusted p-value.	top_hits
Update the model fit by calling the specified fit function only a subset of features. Same design will be fitted.	update_fit