Analyze Results Generated by the 'SqueezeMeta' Pipeline

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Documentation for package ‘SQMtools’ version 1.7.0

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CheckMProkaryote CheckM reference markers for Prokaryotes
combineSQM Combine several SQM objects
combineSQMlite Combine several SQM or SQMlite objects
create_bin Create a bin from a vector of contigs
exportBins Export the bins of a SQM object
exportContigs Export the contigs of a SQM object
exportKrona Export the taxonomy of a SQM object into a Krona Chart
exportORFs Export the ORFs of a SQM object
exportPathway Export the functions of a SQM object into KEGG pathway maps
exportTable Export results in tabular format
find_redundant_contigs Find redundant contigs within a bin
Hadza Hadza hunter-gatherer gut metagenomes
loadSQM Load a SqueezeMeta project into R
loadSQMlite Load tables generated by 'sqm2tables.py', 'sqmreads2tables.py' or 'combine-sqm-tables.py' into R.
MGKOs Single Copy Phylogenetic Marker Genes from Sunagawa's group (KOs)
MGOGs Single Copy Phylogenetic Marker Genes from Sunagawa's group (OGs)
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
plotBars Plot a barplot using ggplot2
plotBins Barplot of the most abundant bins in a SQM object
plotFunctions Heatmap of the most abundant functions in a SQM object
plotHeatmap Plot a heatmap using ggplot2
plotTaxonomy Barplot of the most abundant taxa in a SQM object
RecA RecA/RadA recombinase
remove_contigs_from_bin Remove contigs from a given bin
rowMaxs Return a vector with the row-wise maxima of a matrix or dataframe.
rowMins Return a vector with the row-wise minima of a matrix or dataframe.
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.
subsetContigs Select contigs
subsetFun Filter results by function
subsetORFs Select ORFs
subsetRand Select random ORFs
subsetSamples Filter results by sample
subsetTax Filter results by taxonomy
summary.SQM summary method for class SQM
summary.SQMbunch summary method for class SQMbunch
summary.SQMlite summary method for class SQMlite
USiCGs Universal Single-Copy Genes