Package: rchime 0.1.0

Pat Schloss

rchime: Detect and Remove Chimeras from Amplicon Sequence Analysis Data

Detect and remove chimeras from your amplicon sequence analysis using reference-based or de novo approaches. The 'rchime' package implements the 'VSEARCH' algorithms described in Rognes et al. (2016) <doi:10.7717/peerj.2584>. 'VSEARCH' builds on the work of Edgar,R.C. et al. (2011) <doi:10.1093/bioinformatics/btr381>.

Authors:Sarah Westcott [aut], Pat Schloss [cph, cre], Torbjorn Rognes [cph], Frederic Mahe [cph], Tomas Flouri [cph], Christopher Quince [cph], Ben Nichols [cph]

rchime_0.1.0.tar.gz
rchime_0.1.0.zip(r-4.7-x86_64)rchime_0.1.0.zip(r-4.7-arm64)
rchime_0.1.0.tar.gz(r-4.7-arm64)rchime_0.1.0.tar.gz(r-4.7-x86_64)rchime_0.1.0.tar.gz(r-4.6-arm64)rchime_0.1.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rchime/json (API)

# Install 'rchime' in R:

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

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

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.30 score 4 exports 91 dependencies

Last updated from:5bb9e1c29e. Checks:7 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	211
linux-devel-x86_64	OK	254
source / vignettes	OK	360
linux-release-arm64	OK	217
linux-release-x86_64	OK	252
windows-devel-arm64	OK	428
windows-devel-x86_64	OK	226
wasm-release	FAIL	150

Exports:rchime rchime_example rchime_options silva_gold

Dependencies:ape beeswarm bit bit64 cellranger cli clipr cluster commonmark cpp11 crayon curl data.table diffobj digest dplyr ecodive emmeans estimability farver fillpattern generics ggbeeswarm ggnewscale ggplot2 ggrepel ggtext glue gridtext gtable hms isoband jpeg jsonlite labeling lattice lifecycle litedown magrittr markdown MASS Matrix mgcv microseq mvtnorm nlme numDeriv parallelly patchwork permute pillar pkgconfig plyr png prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rbiom Rcereal RColorBrewer Rcpp RcppThread RcppXsimd readr readxl rematch rlang S7 scales stringi stringr strollur tibble tidyr tidyselect tzdb utf8 vctrs vegan vipor viridisLite vroom waldo withr xfun xml2 yaml

chimera_report

Overview | Example

Rendered fromchimera_report.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
Started: 2026-07-23

De novo Chimera Detection

Rendered fromdenovo_based_detection.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
Started: 2026-07-23

Getting Started

Installing rchime | Tutorials to help you get started

Rendered fromrchime.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
Started: 2026-07-23

Reference Based Chimera Detection

Rendered fromreference_based_detection.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
Started: 2026-07-23

Citation

Readme and manuals

Help Manual

Help page	Topics
Detect and remove chimeras from your strollur object or data.frame using a de novo approach or alternatively a reference model.	rchime
Get path to rchime example files	rchime_example
The 'rchime_options()' function allows you to set vsearch specific optional parameters.	rchime_options
Detect chimeras in your data.frames.	rchime.data.frame
Detect and remove chimeras from your strollur dataset object.	rchime.strollur
silva_gold	silva_gold

Package: rchime 0.1.0

rchime: Detect and Remove Chimeras from Amplicon Sequence Analysis Data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)