Package: strollur 0.1.4

Pat Schloss

strollur: Store and Transfer Amplicon Sequence Data

Stores the data associated with your amplicon sequence analysis. This includes nucleotide sequences, abundance, sample and treatment assignments, taxonomic classifications, asv, otu and phylotype clusters, metadata, trees and various reports. It is designed to facilitate data analysis across multiple R packages with utility functions to read / write from 'mothur', 'qiime2', 'dada2', and 'phyloseq'.

Authors:Sarah Westcott [aut], Gregory Johnson [aut], Pat Schloss [cph, cre]

strollur_0.1.4.tar.gz
strollur_0.1.4.zip(r-4.7-x86_64)strollur_0.1.4.zip(r-4.7-arm64)strollur_0.1.4.zip(r-4.6-x86_64)strollur_0.1.4.zip(r-4.6-arm64)strollur_0.1.4.zip(r-4.5-x86_64)
strollur_0.1.4.tgz(r-4.6-x86_64)strollur_0.1.4.tgz(r-4.6-arm64)strollur_0.1.4.tgz(r-4.5-x86_64)strollur_0.1.4.tgz(r-4.5-arm64)
strollur_0.1.4.tar.gz(r-4.7-arm64)strollur_0.1.4.tar.gz(r-4.7-x86_64)strollur_0.1.4.tar.gz(r-4.6-arm64)strollur_0.1.4.tar.gz(r-4.6-x86_64)
strollur_0.1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
strollur/json (API)

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

Bug tracker:https://github.com/mothur/strollur/issues

Pkgdown/docs site:https://mothur.org

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

amplicon-sequencingasvotusphylogenetic-analysiscpp

6.51 score 1 packages 10 scripts 440 downloads 95 exports 87 dependencies

Last updated from:7d8481681b. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK303
linux-devel-x86_64OK303
source / vignettesOK349
linux-release-arm64OK279
linux-release-x86_64OK335
macos-release-arm64OK310
macos-release-x86_64OK690
macos-oldrel-arm64OK360
macos-oldrel-x86_64OK590
windows-devel-arm64OK440
windows-devel-x86_64OK425
windows-release-arm64OK466
windows-release-x86_64OK358
windows-oldrel-x86_64OK364
wasm-releaseOK154

Exports:abundanceaddassignclearcopy_datasetcountexport_datasetget_bin_typeshas_samplehas_sequence_stringsimport_datasetis_alignedis_equalload_datasetmiseq_sop_examplenamesnew_datasetnew_referenceread_biomread_dada2read_fastaread_fastqread_mothurread_mothur_cons_taxonomyread_mothur_countread_mothur_listread_mothur_oligosread_mothur_rabundread_mothur_sharedread_mothur_taxonomyread_phyloseqread_qiime2read_qiime2_feature_tableread_qiime2_metadataread_qiime2_taxonomyread_qualityreportsave_datasetsort_dataframestrollurstrollur_examplesummaryunpack_qiime2_artifactwrite_biomwrite_fastawrite_fastqwrite_mothurwrite_mothur_cons_taxonomywrite_mothur_countwrite_mothur_designwrite_mothur_listwrite_mothur_rabundwrite_mothur_sharedwrite_phyloseqwrite_qualitywrite_taxonomyxdev_abundancexdev_add_referencesxdev_add_reportxdev_add_sequence_fastq_scoresxdev_add_sequencesxdev_assign_bin_representative_sequencesxdev_assign_bin_taxonomyxdev_assign_bin_taxonomy_tidyxdev_assign_binsxdev_assign_sample_distancesxdev_assign_sequence_abundancexdev_assign_sequence_quality_scoresxdev_assign_sequence_taxonomyxdev_assign_sequence_taxonomy_tidyxdev_assign_treatmentsxdev_countxdev_get_abundances_by_samplexdev_get_alignment_lengthxdev_get_bin_abundances_by_samplexdev_get_by_samplexdev_get_list_vectorxdev_get_sample_distancesxdev_get_sequence_abundances_by_samplexdev_get_sequence_indexes_by_samplexdev_get_sequencesxdev_has_bin_taxonomyxdev_has_sequence_taxonomyxdev_merge_binsxdev_merge_sequencesxdev_namesxdev_remove_binsxdev_remove_lineagesxdev_remove_samplesxdev_remove_sequencesxdev_reportxdev_set_abundancexdev_set_abundancesxdev_set_dataset_namexdev_set_sequences

Dependencies:apebeeswarmbitbit64cellrangerclicliprclustercommonmarkcpp11crayoncurldata.tablediffobjdigestdplyrecodiveemmeansestimabilityfarverfillpatterngenericsggbeeswarmggnewscaleggplot2ggrepelggtextgluegridtextgtablehmsisobandjpegjsonlitelabelinglatticelifecyclelitedownmagrittrmarkdownMASSMatrixmgcvmicroseqmvtnormnlmenumDerivpatchworkpermutepillarpkgconfigplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rbiomRcerealRColorBrewerRcppreadrreadxlrematchrlangS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsveganviporviridisLitevroomwaldowithrxfunxml2yaml

Accessing Data
Overview | Loading the example dataset | Accessing Your Data | strollur::names | strollur::count | strollur::abundance | strollur::report | strollur::summary
Rendered fromAccessing_Dataset.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-02-03

Data Transfers
Saving and Loading | Export and Import | Copy
Rendered fromData_Transfers.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-01-08

Example Analysis Across Software Tools
Overview | Import from mothur | Classify using phylotypr | Diversity Analysis using phyloseq | Create publication-ready plots grouped by treatment | Plot the Shannon Alpha Diversity as a boxplot: | Plot PCoA Beta Diversity: | Deep Dive
Rendered fromExample_Analysis_Across_Software_Tools.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-05-19

Functions for package developers
Under The Hood | Setting functions | Setting the dataset name | Setting nucleotide sequence strings | Setting sequence abundances | Merging Functions | Removing Functions | Removing Sequences | Removing Bins | Removing Samples
Rendered fromFunctions_for_Package_Developers.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-01-08

General Importing
Creating a new dataset | Importing Data | strollur::add | Adding FASTA sequences | Adding Custom Reports | Adding Metadata | Adding Resource References | Adding Trees | strollur::assign | Assigning Abundances | Assigning Bins | Assigning Taxonomic Classifications | Assigning Bin Representatives | Assigning Treatments
Rendered fromGeneral_Importing.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-02-03

Getting Started
Installing strollur | Importing, Accessing and Transfering Data
Rendered fromstrollur.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-02-05

Importing from mothur
Using strollur::read_mothur() | Importing Individual Files | Writing mothur formatted file types
Rendered fromImporting_from_mothur.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-02-03

Importing from phyloseq
Rendered fromImporting_from_phyloseq.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-03-20

Importing from qiime2
Reading Individual Files
Rendered fromImporting_from_qiime2.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2026-02-03

Readme and manuals

Help Manual

Help pageTopics
Get the abundance data for sequences, bins, samples, and treatments in a strollur objectabundance
Add sequences, reports, trees or resource references to a strollur objectadd
Assign sequence abundances, sequence classifications, bins, bin representative sequences, bin classifications, sample distances or treatments to a strollur objectassign
Clear data from a strollur objectclear
Create a new strollur object from an existing dataset.copy_dataset
Find the number of sequences, samples, treatments or bins of a given type in a strollur objectcount
Create a human readable table containing all data from a strollur object.export_dataset
Get bin table types of a strollur objectget_bin_types
Determine if a given sample is in a strollur objecthas_sample
Determine if a strollur object contains sequence nucleotide strings.has_sequence_strings
Create a strollur object from the exported table of a strollur objectimport_dataset
Determine if a strollur object contains aligned sequences.is_aligned
Determine if two strollur objects are equal.is_equal
Load a strollur object from a file.load_dataset
Create a strollur object using the analysis files from the MiSeq_SOP example.miseq_sop_example
Get the names of various data in a strollur objectnames
Create a new strollur objectnew_dataset
Create a resource reference for your strollur object to aid in reproducibility.new_reference
Create a strollur object from a biom formatted file.read_biom
Create a strollur object from dada2 outputsread_dada2
Read a FASTA formatted sequence fileread_fasta
Read a FASTQ formatted fileread_fastq
Create a strollur object from mothur outputsread_mothur
Read a mothur formatted cons_taxonomy fileread_mothur_cons_taxonomy
Read a mothur formatted count fileread_mothur_count
Read a mothur formatted list fileread_mothur_list
Read a mothur formatted oligos fileread_mothur_oligos
Read a mothur formatted rabund fileread_mothur_rabund
Read a mothur formatted shared fileread_mothur_shared
Read a mothur formatted taxonomy fileread_mothur_taxonomy
Create a strollur object from a phyloseq objectread_phyloseq
Create a strollur object from a qiime2 outputsread_qiime2
Read a qiime2 qza containing bin dataread_qiime2_feature_table
Read a qiime2 .tsv table containing metadata.read_qiime2_metadata
Read a qiime2 qza containing taxonomy dataread_qiime2_taxonomy
Read a file containing sequence quality scoresread_quality
remove_fileremove_file
Get a data.frame containing the given report in a strollur objectreport
Save the strollur object to file.save_dataset
sort_dataframesort_dataframe
The 'strollur::strollur' objectstrollur
strollur_examplestrollur_example
Summarize the sequences data, custom reports, and scrapped data in a strollur objectsummary
The unpack_qiime2_artifact function reads .qza files created by qiime2, and returns the artifact.unpack_qiime2_artifact
Write a BIOM formatted file containing a strollur object's data.write_biom
Write a FASTA formatted sequence filewrite_fasta
Write a FASTQ formatted filewrite_fastq
Write the various file types from your strollur object for use with mothur.write_mothur
Write a mothur formatted cons_taxonomy filewrite_mothur_cons_taxonomy
Write a mothur formatted count filewrite_mothur_count
Write a mothur formatted design filewrite_mothur_design
Write mothur formatted list fileswrite_mothur_list
Write mothur formatted rabund fileswrite_mothur_rabund
Write mothur formatted shared fileswrite_mothur_shared
Create a phyloseq object from your strollur objectwrite_phyloseq
Write a file containing sequence quality scoreswrite_quality
Write a 2 column taxonomy filewrite_taxonomy
Get a data.frame containing the requested abundance dataxdev_abundance
Add resource references to a strollur object to aid in reproducibilityxdev_add_references
Add a report to a strollur objectxdev_add_report
Add FASTQ data to a strollur objectxdev_add_sequence_fastq_scores
Add sequence data to a strollur objectxdev_add_sequences
Assign representative sequences to binsxdev_assign_bin_representative_sequences
Assign bin classifications to a strollur objectxdev_assign_bin_taxonomy
Assign bin classifications to a strollur objectxdev_assign_bin_taxonomy_tidy
Add bin assignments to a strollur objectxdev_assign_bins
Assign samples distances in a strollur objectxdev_assign_sample_distances
Assign sequence abundance and optionally assign sample and treatment data to a strollur objectxdev_assign_sequence_abundance
Add quality data to a strollur objectxdev_assign_sequence_quality_scores
Assign sequence classifications to a strollur objectxdev_assign_sequence_taxonomy
Assign sequence classifications to a strollur objectxdev_assign_sequence_taxonomy_tidy
Assign samples to treatments in a strollur objectxdev_assign_treatments
Find the number of sequences, samples, treatments or bins of a given type in a strollur objectxdev_count
Get the sequence abundance data in a strollur object parsed by samplexdev_get_abundances_by_sample
Get the alignment length of sequences in your strollur objectxdev_get_alignment_length
Get the sequence abundance data in a strollur object parsed by samplexdev_get_bin_abundances_by_sample
Get the requested data in a strollur object parsed by samplexdev_get_by_sample
Get vector of strings containing the sequences bin dataxdev_get_list_vector
Get distances between samples in your `strollur objectxdev_get_sample_distances
Get the sequence abundance data in a strollur object parsed by samplexdev_get_sequence_abundances_by_sample
Get indexes of sequences parsed by samplexdev_get_sequence_indexes_by_sample
Get the nucleotide strings for each sequence in a strollur objectxdev_get_sequences
Determine if a strollur object has bin taxonomy assignmentsxdev_has_bin_taxonomy
Determine if a strollur object has sequence taxonomy assignmentsxdev_has_sequence_taxonomy
Merge bins in your strollur objectxdev_merge_bins
Merge sequences combines the abundances of sequencesxdev_merge_sequences
Get the names of a given type of data in a strollur objectxdev_names
Remove bins from a strollur objectxdev_remove_bins
Remove contaminants from a strollur objectxdev_remove_lineages
Remove samples from a strollur objectxdev_remove_samples
Remove sequences from a strollur objectxdev_remove_sequences
Get a data.frame containing the given report in a strollur objectxdev_report
Set abundances of sequences in a strollur object without sample dataxdev_set_abundance
Set abundances of sequences in a strollur object with sample dataxdev_set_abundances
Set the name of a strollur objectxdev_set_dataset_name
Set neucleotide sequence string in a strollur objectxdev_set_sequences