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SQMtools (version 1.7.2)

Analyze Results Generated by the 'SqueezeMeta' Pipeline

Description

'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (). 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) .

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Install

install.packages('SQMtools')

Monthly Downloads

634

Version

1.7.2

License

GPL-3

Issues

20

Pull Requests

0

Stars

421

Forks

84

Maintainer

Fernando Puente-Sánchez

Last Published

June 14th, 2025

Functions in SQMtools (1.7.2)

exportTable

Export results in tabular format
exportORFs

Export the ORFs of a SQM object
loadSQM

Load a SqueezeMeta project into R
find_redundant_contigs

Find redundant contigs within a bin
exportPathway

Export the functions of a SQM object into KEGG pathway maps
create_bin

Create a bin from a vector of contigs
loadSQMlite

Load tables generated by sqm2tables.py, sqmreads2tables.py or combine-sqm-tables.py into R.
exportContigs

Export the contigs of a SQM object
exportKrona

Export the taxonomy of a SQM object into a Krona Chart
exportBins

Export the bins of a SQM object
mostAbundant

Get the N most abundant rows (or columns) from a numeric table
mostVariable

Get the N most variable rows (or columns) from a numeric table
plotTaxonomy

Barplot of the most abundant taxa in a SQM object
seqvec2fasta

Print a named vector of sequences as a fasta-formatted string
subsetBins

Create a SQM object containing only the requested bins, and the contigs and ORFs contained in them.
remove_contigs_from_bin

Remove contigs from a given bin
subsetFun

Filter results by function
subsetContigs

Select contigs
plotFunctions

Heatmap of the most abundant functions in a SQM object
plotHeatmap

Plot a heatmap using ggplot2
subsetSamples

Filter results by sample
subsetTax

Filter results by taxonomy
summary.SQMlite

summary method for class SQMlite
subsetRand

Select random ORFs
subsetORFs

Select ORFs
rowMins

Return a vector with the row-wise minima of a matrix or dataframe.
summary.SQM

summary method for class SQM
plotBins

Barplot of the most abundant bins in a SQM object
summary.SQMbunch

summary method for class SQMbunch
rowMaxs

Return a vector with the row-wise maxima of a matrix or dataframe.
plotBars

Plot a barplot using ggplot2
CheckMProkaryote

CheckM reference markers for Prokaryotes
combineSQM

Combine several SQM objects
SQM_to_microeco

Convert a SQM object into a microtable object from the microeco package
combineSQMlite

Combine several SQM or SQMlite objects
SQM_to_phyloseq

Convert a SQM object into a phyloseq object from the phyloseq package
MGOGs

Single Copy Phylogenetic Marker Genes from Sunagawa's group (OGs)
USiCGs

Universal Single-Copy Genes
Hadza

Hadza hunter-gatherer gut metagenomes
RecA

RecA/RadA recombinase
MGKOs

Single Copy Phylogenetic Marker Genes from Sunagawa's group (KOs)