Package: SQMtools 1.7.0
Fernando Puente-Sánchez
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>.
Authors:
SQMtools_1.7.0.tar.gz
SQMtools_1.7.0.tar.gz(r-4.5-noble)SQMtools_1.7.0.tar.gz(r-4.4-noble)
SQMtools_1.7.0.tgz(r-4.4-emscripten)SQMtools_1.7.0.tgz(r-4.3-emscripten)
SQMtools.pdf |SQMtools.html✨
SQMtools/json (API)
| # Install 'SQMtools' in R: |
| install.packages('SQMtools', repos = 'https://cloud.r-project.org') |
Bug tracker:https://github.com/jtamames/squeezemeta/issues
- CheckMProkaryote - CheckM reference markers for Prokaryotes
- Hadza - Hadza hunter-gatherer gut metagenomes
- MGKOs - Single Copy Phylogenetic Marker Genes from Sunagawa's group
- MGOGs - Single Copy Phylogenetic Marker Genes from Sunagawa's group
- RecA - RecA/RadA recombinase
- USiCGs - Universal Single-Copy Genes
Last updated 15 hours agofrom:d868fcf339. Checks:3 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 31 2025 |
| R-4.5-linux | OK | Mar 31 2025 |
| R-4.4-linux | OK | Mar 31 2025 |
Exports:combineSQMcombineSQMlitecreate_binexportBinsexportContigsexportKronaexportORFsexportPathwayexportTablefind_redundant_contigsloadSQMloadSQMlitemostAbundantmostVariableplotBarsplotBinsplotFunctionsplotHeatmapplotTaxonomyremove_contigs_from_binrowMaxsrowMinsseqvec2fastasubsetBinssubsetContigssubsetFunsubsetORFssubsetRandsubsetSamplessubsetTax
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemclicolorspacecpp11crayoncurldata.tableDBIfansifarverfastmapgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegraphgtablehttrIRangesisobandjsonliteKEGGgraphKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpathviewpillarpkgconfigplogrplyrpngR6RColorBrewerRcppRCurlreshape2RgraphvizrlangRSQLiteS4VectorsscalesstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectorzip
Citation
Puente-Sánchez F., García-García N. and Tamames J., SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o. BMC Bioinformatics 21, 358 (2020).<doi:10.1186/s12859-020-03703-2>.
Corresponding BibTeX entry:
@Article{,
title = {SQMtools: automated processing and visual analysis of
'omics data with R and anvi'o},
author = {{Puente-Sánchez} and {Fernando} and {García-García} and
{Natalia} and {Tamames} and {Javier}},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {1--11},
year = {2020},
publisher = {BioMed Central},
}