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Rsearch (version 1.0.0)

Processing and Analyzing Amplicon Sequence Data

Description

Processing and analysis of targeted sequencing data. The package provides a user-friendly interface for core 'VSEARCH' (Rognes et al. (2016), ) functions, in addition to tools for visualization and parameter tuning.

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Install

install.packages('Rsearch')

Monthly Downloads

139

Version

1.0.0

License

GPL (>= 3)

Issues

0

Pull Requests

0

Stars

1

Forks

1

Maintainer

Cassandra Stamsaas

Last Published

October 26th, 2025

Functions in Rsearch (1.0.0)

taxonomy_tree

Make a taxonomy tree
vs_fastx_uniques

Dereplicate sequences
vs_fastq_join

Join paired-end sequence reads
vs_fastx_trim_filt

Trim and/or filter sequences in FASTA/FASTQ format
vs_cluster_unoise

Denoising FASTA sequences
vs_alignment_classification

Taxonomic classification with LCA
vs_optimize_truncqual

Optimize read truncation with truncqual
vs_search_exact

Search for exact full-length matches
vsearch

Test if VSEARCH can be executed
vs_merging_lengths

Length statistics after merging
vs_optimize_truncee_rate

Optimize read truncation with truncee_rate
vs_sintax

Taxonomic classification using the Sintax algorithm
vs_uchime_denovo

Detect chimeras without external references (i.e. de novo)
vs_fastq_mergepairs

Merge paired-end sequence reads
vs_uchime_ref

Detect chimeras by comparing sequences to a reference database
vs_usearch_global

Global pairwise alignment
vs_fastx_subsample

Subsample sequences
plot_read_quality

Plot read length vs. read quality
plot_size_dist

Plot distribution of size values
phyloseq2rsearch

Convert phyloseq object to Rsearch object
fastx_synchronize

Synchronize FASTA and FASTQ files or objects
plot_base_quality

Plot quality scores per position for FASTQ reads
rsearch2phyloseq

Convert Rsearch object to phyloseq object
plot_ee_rate_dist

Plot distribution of expected error (EE) rate of reads
make_sintax_db

Make Sintax database
fastx_combine_files

Combine FASTA/FASTQ files in a directory into a single file or object
Rsearch-package

Rsearch
rsearch_obj

Create Rsearch object
vs_cluster_subseq

Cluster FASTA sequences
set_vsearch_executable

Set the VSEARCH executable
vs_cluster_size

Cluster FASTA sequences