Package: SQMtools
Title: Analyze Results Generated by the 'SqueezeMeta' Pipeline
Version: 1.8.1
Authors@R: c( 
             person("Fernando", "Puente-Sánchez", email = "fernando.puente.sanchez@slu.se", role = c("aut", "cre")),
             person("Natalia", "García-García", email = "ngarcia@cnb.csic.es", role = c("aut")) 
            )
Description: '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>.
Author: Fernando Puente-Sánchez [aut, cre], Natalia García-García [aut]
Maintainer: Fernando Puente-Sánchez <fernando.puente.sanchez@slu.se>
Depends: R (>= 3.5.0)
biocViews:
LazyDataCompression: xz
Imports: zip, reshape2, ggplot2, pathview, data.table, Biostrings
Suggests: vegan, microeco, phyloseq
License: GPL-3
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/jtamames/SqueezeMeta/issues
URL: https://github.com/jtamames/SqueezeMeta
Config/roxygen2/version: 8.1.0
NeedsCompilation: no
Packaged: 2026-09-26 07:02:43 UTC; root
Config/pak/sysreqs: zlib1g-dev
Repository: https://cran.r-universe.dev
Date/Publication: 2026-08-27 10:00:48 UTC
RemoteUrl: https://github.com/cran/SQMtools
RemoteRef: HEAD
RemoteSha: 5d2df5cabe9a26ab88f069f63f6912ebc31f6143
