Package: Rsearch 1.0.0

Cassandra Stamsaas

Rsearch: Processing and Analyzing Amplicon Sequence Data

Processing and analysis of targeted sequencing data. The package provides a user-friendly interface for core 'VSEARCH' (Rognes et al. (2016), <doi:10.7717/peerj.2584>) functions, in addition to tools for visualization and parameter tuning.

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

Rsearch_1.0.0.tar.gz
Rsearch_1.0.0.zip(r-4.7)Rsearch_1.0.0.zip(r-4.6)Rsearch_1.0.0.zip(r-4.5)
Rsearch_1.0.0.tgz(r-4.6-any)Rsearch_1.0.0.tgz(r-4.5-any)
Rsearch_1.0.0.tar.gz(r-4.7-any)Rsearch_1.0.0.tar.gz(r-4.6-any)
Rsearch_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
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:

16s amplicon bioinformatics clustering denoising fasta fastq metabarcoding metabarcoding-pipeline otu pipeline sintax unoise vsearch

5.01 score 1 stars 20 scripts 156 downloads 31 exports 107 dependencies

Last updated from:27995c9042. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	192
source / vignettes	OK	196
linux-release-x86_64	ERROR	184
macos-release-arm64	ERROR	140
macos-oldrel-arm64	ERROR	184
windows-devel	ERROR	162
windows-release	ERROR	186
windows-oldrel	ERROR	143
wasm-release	OK	138

Exports:fastx_combine_files fastx_synchronize make_sintax_db phyloseq2rsearch plot_base_quality plot_ee_rate_dist plot_read_quality plot_size_dist rsearch_obj rsearch2phyloseq set_vsearch_executable taxonomy_distance taxonomy_tree vs_alignment_classification vs_cluster_size vs_cluster_subseq vs_cluster_unoise vs_fastq_join vs_fastq_mergepairs vs_fastx_subsample vs_fastx_trim_filt vs_fastx_uniques vs_merging_lengths vs_optimize_truncee_rate vs_optimize_truncqual vs_search_exact vs_sintax vs_uchime_denovo vs_uchime_ref vs_usearch_global vsearch

Dependencies:ade4 ape base64enc Biobase BiocGenerics biomformat Biostrings bit bit64 bslib cachem cli clipr cluster codetools colourpicker commonmark cowplot cpp11 crayon data.table digest dplyr evaluate farver fastmap fontawesome foreach fs generics ggExtra ggplot2 glue gtable highr hms htmltools htmlwidgets httpuv igraph IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv microseq mime miniUI multtest nlme otel permute phyloseq pillar pixmap pkgconfig plyr prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr reshape2 rlang rmarkdown S4Vectors S7 sass scales Seqinfo shiny shinyjs sourcetools sp stringi stringr survival tibble tidyr tidyselect tinytex tzdb utf8 vctrs vegan viridisLite vroom withr xfun xtable XVector yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Combine FASTA/FASTQ files in a directory into a single file or object	fasta_combine_files fastq_combine_files fastx_combine_files
Synchronize FASTA and FASTQ files or objects	fasta_synchronize fastq_synchronize fastx_synchronize
Make Sintax database	make_sintax_db sintax_db
Convert phyloseq object to Rsearch object	phyloseq2rsearch
Plot quality scores per position for FASTQ reads	plot_base_quality
Plot distribution of expected error (EE) rate of reads	plot_ee_rate_dist
Plot read length vs. read quality	plot_read_quality
Plot distribution of size values	plot_size_dist
Create Rsearch object	rsearch_obj
Convert Rsearch object to phyloseq object	rsearch2phyloseq
Set the VSEARCH executable	set_vsearch_executable
Creates a distance object based on taxonomy information.	taxonomy_distance
Make a taxonomy tree	taxonomy_tree
Taxonomic classification with LCA	alignment_classification lca lca_classification vs_alignment_classification
Cluster FASTA sequences	cluster cluster_size vs_cluster vs_cluster_size
Cluster FASTA sequences	vs_cluster_length vs_cluster_subseq
Denoising FASTA sequences	cluster_unoise denoise unoise vs_cluster_unoise
Join paired-end sequence reads	fastq_join join vs_fasta_join vs_fastq_join vs_fastx_join
Merge paired-end sequence reads	fastq_mergepairs mergepairs vs_fasta_mergepairs vs_fastq_mergepairs vs_fastx_mergepairs vs_mergepairs
Subsample sequences	fastx_subsample subsample vs_fasta_subsample vs_fastq_subsample vs_fastx_subsample vs_subsample
Trim and/or filter sequences in FASTA/FASTQ format	fastx_trim_filt trim_filt vs_fasta_trim_filt vs_fastq_trim_filt vs_fastx_trim_filt
Dereplicate sequences	dereplicate fastx_uniques vs_fasta_dereplicate vs_fasta_uniques vs_fastq_dereplicate vs_fastq_uniques vs_fastx_dereplicate vs_fastx_uniques
Length statistics after merging	merging_lengths vs_merging_lengths
Optimize read truncation with truncee_rate	optimize_truncee_rate vs_optimize_truncee_rate
Optimize read truncation with truncqual	optimize_truncqual vs_optimize_truncqual
Search for exact full-length matches	search_exact vs_search_exact
Taxonomic classification using the Sintax algorithm	classify 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 database	uchime_ref vs_uchime_ref
Global pairwise alignment	global_alignment usearch_global vs_usearch_global
Test if 'VSEARCH' can be executed	vsearch