Name	Short Description	Language
ABRGeneLength	Length of antibacterial resistant genes	Python
ALC	Approximate line count	C++
Accuracy	Prediction accuracy	R
AntibioticBox	Boxplot of antibiotic resistant taxa abundances	R
Atima	Atima (Weick et al, 2000) (Generated by PluGen)	C++
AUC	Area under the curve	Python
AUPRCMultiple	Area under precision recall curve (multiple)	Python
AverageDistance	Compute average distance	Python
BAMCoverage	Compute coverage of a BAM file	C++
BAMDepth	Compute depth of a BAM file	C++
BamHash	Generate a checksum for a FASTA (Oskarsdottir et al, 2016)	C++
BAMStats	Take a BAM as input and output stats (Barnett et al, 2011)	C++
Banner	Customizeable software banner	Python
BenjaminiHochberg	Benjamini-Hochberg p-value correction (Benjamini and Hochberg, 1995)	Python
BlandAltman	Bland-Altman plot (Bland and Altman, 1983)	Python
BLASTFreq	Most frequent BLAST hits	C++
BLASTTop	Top BLAST hits	C++
BlockPlot	Block	R
Bonferroni	Bonferroni p-value correction (Bonferroni, 1936)	Python
BoxPlot	Produce a boxplot	R
BoxSelect	Produce multiple boxplots of selected data elements	R
BoxWhisker	Box-and-whisker plot	Python
BWPlot	Box and whisker plot	R
CalcMeanStd	Calculates Mean and Standard Deviation	Python
CalibrationCurve	Characterize consistency between class probabilities and event rates	R
ClosestBed	Find closest BED	C++
ContigStats	Contig stats	C++
CountPlot	Plot of counts	Python
CQNPlot	Conditional Quantile Normalization Plot (Wu et al, 2012)	R
CSVAverage	Average column values of a CSV file	Python
CSVCheck	Check for validity, and number of observables	Python
CSVDup	List duplicate row and column entries in a CSV file.	Python
CSVMax	Determines Maximum Count Within Samples	Python
CSVOverlap	Vector overlap	Python
CheckSignificance	Check significance of result	Python
CountReads	Count number of reads	Python
CoverageBed	Calculate the coverage of mapped reads at each location on the reference genome (Liao et al, 2013)	C++
CoveragePlot	Plot read coverage	R
DenNHist	Density plot (q-values)	R
Density	Density plot (normalized abundance vs frequency) of a target taxon	R
DensityOverlay	Density overlay plot	R
DensityPlot	Density plot (general)	R
DeterminePhred	Determine Phred score	C++
DimHeatmap	Dimensionality heatmap	R
DimPlot	Dimensionality plot	R
DivideHighLow	Separate taxa into highly and lowly abundant	Python
DMDSPlot	DMDS Plot (Nowicka et al, 2016)	R
Dominance	Dominance index (Locey and Lennon, 2016)	R
DotPlot	Dot plot	R
DoubleTest	Double a list of values	Python
ElbowPlot	Elbow plot	R
ErrorRate	Error statistics in sequence bases	R
Evenness	Evenness indices	R
FASTACount	Count the number of sequences in a FASTA file	Python
FASTAStats	FASTA file statistics	Python
FASTQStats	Stats on FASTQ file	C++
FeaturePlot	Feature plot	R
FeatureScatter	Feature scatter plot	R
FValue	F-statistic	R
GCMAPlot	GCMA plot	R
GCContig	Count 'G', 'C' bases in a set of contigs	C++
GCStats	Count 'G', 'C' bases	C++
GOHeatmap	Produce heatmap using Gene Ontology (Thomas et al, 2022)	R
GeneList	Produce list of genes	R
GeneTable	Produce table of genes	R
GetPatterns	Get patterns over a set of conditions	R
Gini	Gini index (Gini, 1912)	R
GLMCommonDisp	Estimate GLM common dispersion	R
Gnuplot	Plot data using Gnuplot (Williams and Kelley, 2011)	C++
GroupBox	GroupBox plot	R
HeatmapPTR	Heatmap for Peak-to-Trough Ratio (PTR) analysis	R
HighHit	High and low bacteria hits	Perl
Hilbert	Hilbert curve (Hilbert, 1891)	R
Histogram	Generate histogram	R
HistogramScore	Plot scores as Histogram	R
IdentityPlot	Identity plot	R
IntersectBed	BED file intersection	C++
JasperBanner	Jasper software banner (Valdes et al, 2020)	Python
JointROCC	Joint Receiver Operating Characteristic Curve	Python
Kappa	Kappa statistic (Cohen, 1960)	R
KDE	KDE plot	Python
KronaCount	Count the number of taxa in a Krona file	Python
KS	Kolmogorov-Smirnov Test Statistic (Kolmogorov, 1933)	R
LabeledBox	Boxplot based on sample classification	Python
LiftCurve	Probability thresholds that capture hit percentages	R
Likelihood	Compute likelihood	R
LinePlot	Line Plot (Nowicka et al, 2016)	R
LogFoldScale	Log-fold scale analysis	Python
LogModulo	Log-modulo skew (Magurran and McGill, 2011)	R
LongestContig	Find the longest contig in a FASTA file	Python
MannWhitney	Mann-Whitney Test (Mann and Whitney, 1947)	Python
MannWhitneyPValue	P-value for Mann-Whitney Test (Mann and Whitney, 1947)	Python
MedianNorm	Median by ratio normalization (Anders et al, 2010)	R
MIMOSA	Data fitting through MIMOSA (Finak et al, 2013)	R
MIQ	Median InterQuartile (IQ)	Python
MULTIQC	Summarize results from multiple bioinformatics toolkits in HTML form (Ewels et al, 2016) (Generated by PluGen)	C++
MV	Plot mean vs. variance	R
Mantel	Mantel test (Diniz-Filho et al, 2013)	R
OTURecover	Number of OTUs recovered	Python
OTUSummary	Summarize OTUs at multiple levels of the phylogenetic tree	C++
Ontology	Ontology summary	Perl
PairedPValue	Paired p-value	Python
PanChromosome	Panchromosome visualization	Perl
PhredBox	Box plot of Phred score	R
Phylum	Map taxa to phylum	Python
PhylumQiime	List phyla from Qiime input	Python
Plot2TX	Plot transcript proportion difference	R
PlotCV	Plot co-variance	Python
PlotExpression	Plot gene expression levels	R
PlotFC	Plot fold change accuracy	R
PlotFI	Plot feature importancer	Python
PlotFoldChange	Plot fold-change	R
PlotGC	GC plot	R
PlotHMP	Plotter for HMP data	R
PlotNA	NA-distribution plot	R
PlotNE	Estimate and plot express and non-express features	R
PlotPosterior	Plot posterior density	R
PlotROC	Plot Receiver Operating Characteristic Curve	R
PlotROCC	Plot Receiver Operating Characteristic Curve (Uses AUC)	Python
PlotSD	Estimate and plot medium standard deviation	R
PlotTSNE	TSNE plot (van der Maaten, 2008)	Python
PlotUnivariate	Plot univariate effects	R
Plotly	Plot data using Plotly (Plotly Technologies, Inc.)	R
PlotlySorted	Plot sorted data using Plotly (Plotly Technologies, Inc.)	R
PlotMarker	Plot marker genes	R
PlusMinus	Calculate number of reads on forward and reverse strand	C++
PairPlot	Pair plot	Python
PolyFitPlot	Polynomial regression plot	R
Posterior	Posterior probability	R
PosteriorFold	Posterior Fold Change	R
PrecisionRecall	Precision recall curve	R
Prior	Estimate prior parameters	R
Procrustes	Procrusts analysis (Gower, 1975)	R
PValue	Compute P-Value	Python
PValuePlot	Plot p-values	R
ProportionPlot	Proportion plot	R
Qiime2Viz	Qiime 2 Visualizer (Bolyen et al, 2019) (Generated by PluGen)	C++
QualiMap	Generate a QualiMap (Garcia-Alcalde et al, 2012) report	C++
QualityProfile	Sequence quality statistics	R
QuantileQuantile	QQ plot	R
QuantileScore	Produce quantiles based on set of scores	R
RPKM	Reads of kilobase per transcript per million	R
RPKMPlot	RPKM plot	R
Rare	Rare taxa community statistics	R
ReadTracker	Track reads through a pipeline	R
RibbonPlot	Ribbon plot	R
ROCMultiple	Receiver Operating Characteristic, Multiple (Fawcett, 2006)	R
ScatterEllipse	Scatter plot with ellipses	R
SAMParser	SAM parser, statistics	Python
SAMStats	Miscellaneous SAM statistics	C++
ScatterPair	Scatter plot (pairwise)	R
SelectMajorABR	Select antimicrobial resistant taxa	Python
SequenceLength	Sequence length	Python
SGPlot	Splice graph plot	R
SGFPlot	Splice graph feature plot	R
Shear	Combined genome shear	Python
SingleCellHeatmap	Heatmap of single-cell feature expression	R
SNPPlot	Plot SNPs	R
Sparsity	Plot sparsity of a dataset	R
SpeedTest	Machine upload/download speed	C++
SPloM	Scatter plot matrix	R
SquareTest	Square a list of values	Python
StackedBar	Stacked bar plot	R
StackedBarSelect	Stacked bar plot with targetted genes/species	R
Statistics	Take a set of samples and output statistics (mean, standard deviation, etc.) on the most abundant taxa	Python
StripPlot	Plot resampling and tuning parameters	R
SubsetScore	Return subset of scores	R
Summarize	Output a summary of a sample set to the screen	R
SumTest	Sum a list of values	Python
SurrogateP	Surrogate p-value	R
SyntheticAbundance	Generate synthetic abundances	Python
TaxaQuery	Query a taxon and obtain statistics	Python
TetraESOM	Tetramer frequencies, input to ESOM (Dick, 2009) (Generated by PluGen).	C++
TopCounts	Top counts	R
TTestDependent	Run the T-Test on dependent samples	Python
TTestIndependent	Run the T-Test on independent data	Python
TreeStats	Miscellaneous statistics for a taxonomic tree	Python
TrellisScatter	Trellis scatter plot (Trellis, 2017)	R
TrellisSmooth	Trellis plot, smooth (Trellis, 2017)	R
Unclassified	Number of OTUs unclassified	Python
UnclassifiedList	List unclassified OTUs	Python
Unique2One	Collect taxa unique to one set	Python
UniqueCount	Count of unique sequences	C++
UpSetR	UpsetR (Lex et al, 2019) visualization	R
VariableFeaturePlot	Variable feature plot	R
Variance	Variance Calculator	Python
Venn	Venn Diagram	Python
ViolinXY	Violin plot, x-y data	Python
Viridis	Viridis heatmap	Python
VizDimLoadings	Visualize top genes associated with reduction components	R
VlnPlot	Violin feature plot	R
WGEval	Whole genome simulator evaluator tool (WGSim, 2011)	Perl
WGSim	Whole genome simulator evaluator tool (WGSim, 2011)	C++
ZeroPercent	Percent of control samples with zero abundance (helps with power set)	Python
ZScoreScale	Z-score scaling	R

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