Package: SQMtools 1.6.3

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:Fernando Puente-Sánchez [aut, cre], Natalia García-García [aut]

SQMtools_1.6.3.tar.gz
SQMtools_1.6.3.tar.gz(r-4.5-noble)SQMtools_1.6.3.tar.gz(r-4.4-noble)
SQMtools_1.6.3.tgz(r-4.4-emscripten)SQMtools_1.6.3.tgz(r-4.3-emscripten)
SQMtools.pdf |SQMtools.html
SQMtools/json (API)

# Install 'SQMtools' in R:
install.packages('SQMtools', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jtamames/squeezemeta/issues

Datasets:
  • 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

1.36 score 1 stars 23 scripts 387 downloads 24 exports 74 dependencies

Last updated 1 years agofrom:65c7590d79. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-linuxOKNov 12 2024

Exports:combineSQMcombineSQMliteexportKronaexportPathwayexportTableloadSQMloadSQMlitemostAbundantmostVariableplotBarsplotBinsplotFunctionsplotHeatmapplotTaxonomyrowMaxsrowMinsseqvec2fastasubsetBinssubsetContigssubsetFunsubsetORFssubsetRandsubsetSamplessubsetTax

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemclicolorspacecpp11crayoncurldata.tableDBIfansifarverfastmapgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegraphgtablehttrIRangesisobandjsonliteKEGGgraphKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpathviewpillarpkgconfigplogrplyrpngR6RColorBrewerRcppRCurlreshape2RgraphvizrlangRSQLiteS4VectorsscalesstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Combine several SQM objectscombineSQM
Combine several SQM or SQMlite objectscombineSQMlite
Export the taxonomy of a SQM object into a Krona ChartexportKrona
Export the functions of a SQM object into KEGG pathway mapsexportPathway
Export results in tabular formatexportTable
Hadza hunter-gatherer gut metagenomesHadza
Load a SqueezeMeta project into RloadSQM
Load tables generated by 'sqm2tables.py', 'sqmreads2tables.py' or 'combine-sqm-tables.py' into R.loadSQMlite
Single Copy Phylogenetic Marker Genes from Sunagawa's group (KOs)MGKOs
Single Copy Phylogenetic Marker Genes from Sunagawa's group (OGs)MGOGs
Get the N most abundant rows (or columns) from a numeric tablemostAbundant
Get the N most variable rows (or columns) from a numeric tablemostVariable
Plot a barplot using ggplot2plotBars
Barplot of the most abundant bins in a SQM objectplotBins
Heatmap of the most abundant functions in a SQM objectplotFunctions
Plot a heatmap using ggplot2plotHeatmap
Barplot of the most abundant taxa in a SQM objectplotTaxonomy
RecA/RadA recombinaseRecA
Return a vector with the row-wise maxima of a matrix or dataframe.rowMaxs
Return a vector with the row-wise minima of a matrix or dataframe.rowMins
Print a named vector of sequences as a fasta-formatted stringseqvec2fasta
Create a SQM object containing only the requested bins, and the contigs and ORFs contained in them.subsetBins
Select contigssubsetContigs
Filter results by functionsubsetFun
Select ORFssubsetORFs
Select random ORFssubsetRand
Filter results by samplesubsetSamples
Filter results by taxonomysubsetTax
summary method for class SQMsummary.SQM
summary method for class SQMlitesummary.SQMlite
Universal Single-Copy GenesUSiCGs