Have a new plugin that you would like to add to the pool? Please send your source code and a description to Trevor Cickovski. All plugins in the pool will be added as test cases for future releases of PluMA, giving you automatic forward compatibility!

Name |
Short Description |
Language |

AffinityPropagation |
Affinity Propagation (Frey and Dueck, 2007) (Python) | Python |

ATria |
Ablatio Triadum (ATria) Centrality (Cickovski et al, 2017) | C++ |

AutoCorrelation |
Autocorrelation Function Estimate | R |

BiasedPageRank |
Edge-Weighted Personalized Page Rank (Xie et al, 2015) | Python |

Binomial |
Binomial Deviance (McArdle and Anderson, 2001) | R |

Bray |
Bray-Curtis (Bray and Curtis, 1957) | R |

CalcMeanStd |
Calculates Mean and Standard Deviation | Python |

Canberra |
Canberra Distance (Lance and Williams, 1966) | R |

Chao |
Chao's Method (Chao, 2005) | R |

Classify |
Phylogenetic OTU Classifier | Python |

ClusterCSV2NOA |
Convert CSV File Of Clusters to NOA | Python |

Clusterize |
Remove Edges Between Nodes in Different Clusters | Python |

CountTableProcessing |
Converts Mothur Counts To Abundance CSV | R |

CrossCorrelation |
Time-Series Cross-Correlation Values | R |

CSV2GML |
CSV To GML Converter | Python |

CSVMapRange |
Map Range of One CSV File To Another (Useful in Multi-Omics) | Python |

CSVNeg2Zero |
Change Negative Edges To Zero | Python |

CSVNormalize |
CSV Normalization | Python |

CSVPad |
CSV Padding | Python |

CSVScale |
Scale CSV Values to Have a Median of One | Python |

CSVTranspose |
Transpose a Matrix in a CSV File | Python |

CSVZero2Min |
Change All Zeroes in a CSV to the Minimum Value | Python |

Cytoscape |
Cytoscape Visualizer (Shannon et al, 2003) (Generated by PluGen) | C++ |

CytoViz |
Cytoscape Visualizer | Perl |

Degree |
Degree Centrality (Freeman, 1979) | C++ |

Detrend |
Detrend (Least-Squares Fit, Time Series Data) | R |

DickeyFuller |
Dickey-Fuller Test, Time Series Data (Said and Dickey, 1984) | R |

DistanceCorrelation |
Distance Correlation (Szekely, 2005) | R |

EuclideanDistance |
Euclidean Distance | R |

Exponential |
Exponential Centality (Benzi and Klymko, 2013) | Python |

Gower |
Gower Index (Gower, 1971) | R |

GPUATria |
GPUATria (ATria, on the GPU) | CUDA |

Horn |
Horn's Overlap Index (Horn, 1966) | R |

InverseSimpson |
Inverse Simpson Diversity Index | Python |

Jaccard |
Jaccard Index (Jaccard, 1912) | R |

Katz |
Katz Prestige Centrality (Katz, 1953) | C++ |

Kendall |
Kendall Correlation (Kendall, 1970) | R |

Kulczynski |
Kulczynski Similarity (Kulczynski, 1927) | R |

LSA |
Local Similarity Analysis (Ruan, 2006) | Python |

MakeCliques |
Make a Network of Cliques (Python) | Python |

MakeSynthetic |
Make a Synthetic Network | Python |

Manhattan |
Manhattan Distance | R |

Map2Positive |
Map All Edges To Positive Range | Python |

MATria |
Multiple Ablatio Triadium (Cickovski et al, 2017) | Python |

MCL |
Markov Clustering (van Dongen, 2000) | R |

MIC |
Maximal Information Coefficient (Reshef, 2011) | R |

MetaBAT |
MetaBAT (Kang et al, 2015) (Generated by PluGen) | C++ |

ModularityMaximization |
Modularity Maximization Algorithm For Clustering Level | Python |

Morisita |
Morisita Overlap (Morisita, 1959) | R |

Mothur |
Mothur (Schloss, 2009) (Generated by PluGen) | C++ |

Mountford |
Mountford Dissimilariy Index (Mountford, 1962) | R |

NetworkViz |
Network Visualizer (Generates Multiple Cytoscape Input Files) | Python |

NormScoreTransform |
Normal Probability Values | R |

PageRank |
Page Rank Centrality (Page, 1999) | Python |

PCL2CSV |
PCL To CSV (File Conversion) | Python |

Pearson |
Pearson Correlation (Pearson, 1896) | R |

PyATria |
ATria, in Python | Python |

QGraph |
QGraph Visualizer | R |

Raup |
Raup-Crick (Raup and Crick, 1979) | R |

ReactionPathway |
ReactionPathway (Statistical Analysis of Metabolite Network and Reaction Pathway Data) | Python |

RemoveNegative |
Remove Negative Edges | Python |

SIMLR |
SIMLR (Wang et al, 2017) | R |

Spearman |
Spearman Correlation (Spearman, 1904) | R |

Spectral |
Spectral Clustering (Meila and Shi, 2001) | Python |

Variance |
Variance Calculator | Python |