SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.

Version: 1.6.3
Depends: R (≥ 3.5.0)
Imports: reshape2, ggplot2, pathview, data.table
Suggests: vegan, DESeq2
Published: 2023-09-18
DOI: 10.32614/CRAN.package.SQMtools
Author: Fernando Puente-Sánchez [aut, cre], Natalia García-García [aut]
Maintainer: Fernando Puente-Sánchez <fernando.puente.sanchez at slu.se>
BugReports: https://github.com/jtamames/SqueezeMeta/issues
License: GPL-3
URL: https://github.com/jtamames/SqueezeMeta
NeedsCompilation: no
Citation: SQMtools citation info
CRAN checks: SQMtools results


Reference manual: SQMtools.pdf


Package source: SQMtools_1.6.3.tar.gz
Windows binaries: r-devel: SQMtools_1.6.3.zip, r-release: SQMtools_1.6.3.zip, r-oldrel: SQMtools_1.6.3.zip
macOS binaries: r-release (arm64): SQMtools_1.6.3.tgz, r-oldrel (arm64): SQMtools_1.6.3.tgz, r-release (x86_64): SQMtools_1.6.3.tgz, r-oldrel (x86_64): SQMtools_1.6.3.tgz
Old sources: SQMtools archive


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