Package: Rsearch 1.2.0

Cassandra Stamsaas

Rsearch: Processing and Analyzing Amplicon Sequence Data

Processing and analysis of amplicon sequencing data, with a primary focus on eDNA metabarcoding while remaining applicable to general targeted sequencing workflows. The package provides a user-friendly interface for core 'VSEARCH' (Rognes et al. (2016), <doi:10.7717/peerj.2584>) functions, extended with dedicated tools for visualization and parameter tuning.

Authors:Cassandra Stamsaas [cre, aut], Lars Snipen [aut], Torbjørn Rognes [aut], Hilde Vinje [aut]

Rsearch_1.2.0.tar.gz
Rsearch_1.2.0.zip(r-4.7-any)Rsearch_1.2.0.zip(r-4.6-any)Rsearch_1.2.0.zip(r-4.5-any)
Rsearch_1.2.0.tgz(r-4.6-any)Rsearch_1.2.0.tgz(r-4.5-any)
Rsearch_1.2.0.tar.gz(r-4.7-any)Rsearch_1.2.0.tar.gz(r-4.6-any)
Rsearch_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rsearch/json (API)

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

Bug tracker:https://github.com/cassandrahjo/rsearch/issues

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

On CRAN:

Conda:

16sampliconbioinformaticsclusteringdenoisingfastafastqmetabarcodingmetabarcoding-pipelineotupipelinesintaxunoisevsearch

4.98 score 1 stars 21 scripts 348 downloads 31 exports 80 dependencies

Last updated from:fc3761b028. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR172
source / vignettesOK453
linux-releaseERROR168
macos-releaseERROR201
macos-oldrelERROR169
windows-develERROR132
windows-releaseERROR130
windows-oldrelERROR126
wasm-releaseOK125

Exports:fastx_combine_filesfastx_synchronizemake_sintax_dbphyloseq2rsearchplot_base_qualityplot_ee_rate_distplot_read_qualityplot_size_distrsearch_objrsearch2phyloseqset_vsearch_executabletaxonomy_distancetaxonomy_treevs_alignment_classificationvs_cluster_sizevs_cluster_subseqvs_cluster_unoisevs_fastq_joinvs_fastq_mergepairsvs_fastx_subsamplevs_fastx_trim_filtvs_fastx_uniquesvs_merging_lengthsvs_optimize_truncee_ratevs_optimize_truncqualvs_search_exactvs_sintaxvs_uchime_denovovs_uchime_refvs_usearch_globalvsearch

Dependencies:apebase64encbitbit64bslibcachemclicliprcolourpickercommonmarkcowplotcpp11crayondata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggExtraggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrmemoisemicroseqmimeminiUInlmeotelpillarpkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownS7sassscalesshinyshinyjssourcetoolsstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyaml

Readme and manuals

Help Manual

Help pageTopics
Combine FASTA/FASTQ files in a directory into a single file or objectfasta_combine_files fastq_combine_files fastx_combine_files
Synchronize FASTA and FASTQ files or objectsfasta_synchronize fastq_synchronize fastx_synchronize
Make Sintax databasemake_sintax_db sintax_db
Convert phyloseq object to Rsearch objectphyloseq2rsearch
Plot quality scores per position for FASTQ readsplot_base_quality
Plot distribution of expected error (EE) rate of readsplot_ee_rate_dist
Plot read length vs. read qualityplot_read_quality
Plot distribution of size valuesplot_size_dist
Create Rsearch objectrsearch_obj
Convert Rsearch object to phyloseq objectrsearch2phyloseq
Set the VSEARCH executableset_vsearch_executable
Creates a distance object based on taxonomy information.taxonomy_distance
Make a taxonomy treetaxonomy_tree
Taxonomic classification with LCAalignment_classification lca lca_classification vs_alignment_classification
Cluster FASTA sequencescluster cluster_size vs_cluster vs_cluster_size
Cluster FASTA sequencesvs_cluster_length vs_cluster_subseq
Denoising FASTA sequencescluster_unoise denoise unoise vs_cluster_unoise
Join paired-end sequence readsfastq_join join vs_fasta_join vs_fastq_join vs_fastx_join
Merge paired-end sequence readsfastq_mergepairs mergepairs vs_fasta_mergepairs vs_fastq_mergepairs vs_fastx_mergepairs vs_mergepairs
Subsample sequencesfastx_subsample subsample vs_fasta_subsample vs_fastq_subsample vs_fastx_subsample vs_subsample
Trim and/or filter sequences in FASTA/FASTQ formatfastx_trim_filt trim_filt vs_fasta_trim_filt vs_fastq_trim_filt vs_fastx_trim_filt
Dereplicate sequencesdereplicate fastx_uniques vs_fasta_dereplicate vs_fasta_uniques vs_fastq_dereplicate vs_fastq_uniques vs_fastx_dereplicate vs_fastx_uniques
Length statistics after mergingmerging_lengths vs_merging_lengths
Optimize read truncation with truncee_rateoptimize_truncee_rate vs_optimize_truncee_rate
Optimize read truncation with truncqualoptimize_truncqual vs_optimize_truncqual
Search for exact full-length matchessearch_exact vs_search_exact
Taxonomic classification using the Sintax algorithmclassify sintax vs_sintax
Detect chimeras without external references (i.e. de novo)chimera uchime_denovo vs_uchime_denovo
Detect chimeras by comparing sequences to a reference databaseuchime_ref vs_uchime_ref
Global pairwise alignmentglobal_alignment usearch_global vs_usearch_global
Test if 'VSEARCH' can be executedvsearch