CheckMProkaryote        CheckM reference markers for Prokaryotes
Hadza                   Hadza hunter-gatherer gut metagenomes
MGKOs                   Single Copy Phylogenetic Marker Genes from
                        Sunagawa's group (KOs)
MGOGs                   Single Copy Phylogenetic Marker Genes from
                        Sunagawa's group (OGs)
RecA                    RecA/RadA recombinase
SQM_to_microeco         Convert a SQM object into a microtable object
                        from the _microeco_ package
SQM_to_phyloseq         Convert a SQM object into a phyloseq object
                        from the _phyloseq_ package
USiCGs                  Universal Single-Copy Genes
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
loadSQM                 Load a SqueezeMeta project into R
loadSQMlite             Load tables generated by 'sqm2tables.py',
                        'sqmreads2tables.py' or 'combine-sqm-tables.py'
                        into R.
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
remove_contigs_from_bin
                        Remove contigs from a given bin
renameSamples           Change sample names
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
