PluMA: Plugin-Based Microbiome Analysis

Plugin Pool


These plugins have been tested and are compatible with the latest version of PluMA. You can download just the ones you wish to use.  The easiest way to install them is to place them in the plugins/ directory of the PluMA source tree, however you can install them elsewhere by setting the environment variable PLUMA_PLUGIN_PATH.

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!

File Converters Stats/Visualization Transformations Dissimilarity Correlation Centrality Clustering Time Series External Tools Miscellaneous
File Converters
Name Short Description Language
ClusterCSV2NOA Convert CSV File Of Clusters to NOA Python
CountTableProcessing Converts Mothur Counts To Abundance CSV R
CSV2EDA Converter from CSV to Cytoscape EDA file format Python
CSV2GML CSV To GML Converter Python
CSVMerge Merge Multiple CSV Files Python
CSVPad CSV Padding Python
PCL2CSV PCL To CSV (File Conversion) Python
Stats/Visualization
Name Short Description Language
CalcMeanStd Calculates Mean and Standard Deviation Python
CSV2Dot Take a Network in CSV Format and Visualize in Dot (Gansner et al, 2015) Python
CSVMax Determines Maximum Count Within Samples Python
Cytoscape Cytoscape Visualizer (Shannon et al, 2003) (Generated by PluGen) C++
CytoViz Cytoscape Visualizer Perl
InverseSimpson Inverse Simpson Diversity Index Python
MM Partitions multi-omics data Python
NetworkViz Network Visualizer (Generates Multiple Cytoscape Input Files) Python
QGraph QGraph Visualizer R
ReactionPathway ReactionPathway (Statistical Analysis of Metabolite Network and Reaction Pathway Data) Python
Rank Converts a set of counts to ranks in a sample Python
Variance Variance Calculator Python
Transformations
Name Short Description Language
Clusterize Remove Edges Between Nodes in Different Clusters Python
CSVFilter Remove Columns from a CSV file with All Zero Values Python
CSVMapRange Map Range of One CSV File To Another (Useful in Multi-Omics) Python
CSVNeg2Pos Map [-1, 1] edge weight range to [0, 2] Python
CSVNeg2Zero Change Negative Edges To Zero Python
CSVNormalize CSV Normalization Python
CSVScale Scale CSV Values to Have a Median of One Python
CSVTranspose Transpose a Matrix in a CSV File Python
CSVUnNormalize CSV Reverse Normalization Python
CSVZero2Min Change All Zeroes in a CSV to the Minimum Value Python
FilterMicrobes Filter out connections between metagenomic data based on underlying metabolic networks Python
LogTransform Log-transform data Python
Map2Positive Map All Edges To Positive Range Python
MetabNorm Mixed-Mode (Cohort and Batch) Metabolite Normalization (Jauhiainen et al, 2014) R
NetworkDeconvolution Network deconvolution algorithm (Feizi et al, 2013) to determine direct network dependencies. R
NormScoreTransform Normal Probability Values R
QuantumDenoiser Remove noisy fluctations from CKMeans quanta R
RemoveNegative Remove Negative Edges Python
Transform Shift composition (Egozcue and Pawlowski-Glahn, 2016) Python
Dissimilarity
Name Short Description Language
BinomialDeviance Binomial Deviance (McArdle and Anderson, 2001) R
Bray Bray-Curtis (Bray and Curtis, 1957) R
Canberra Canberra Distance (Lance and Williams, 1966) R
Chao Chao's Method (Chao, 2005) R
EuclideanDistance Euclidean Distance R
Gower Gower Index (Gower, 1971) R
Horn Horn's Overlap Index (Horn, 1966) R
Jaccard Jaccard Index (Jaccard, 1912) R
Kulczynski Kulczynski Similarity (Kulczynski, 1927) R
Manhattan Manhattan Distance R
Morisita Morisita Overlap (Morisita, 1959) R
Mountford Mountford Dissimilariy Index (Mountford, 1962) R
Raup Raup-Crick (Raup and Crick, 1979) R
Correlation
Name Short Description Language
DistanceCorrelation Distance Correlation (Szekely, 2005) R
Ensemble Ensemble Correlation Computation (Weiss, 2016) Python
FunChiSq Functional Chi-Squared Dependency Computation (Zhang and Song, 2013) R
Kendall Kendall Correlation (Kendall, 1970) R
LSA Local Similarity Analysis (Ruan, 2006) Python
MIC Maximal Information Coefficient (Reshef, 2011) R
Pearson Pearson Correlation (Pearson, 1896) R
Phi Proportionatlity metric (Lovell et al, 2015) for relative data Python
SparCC SparCC Correlation (Friedman and Alm, 2012) Python
Spearman Spearman Correlation (Spearman, 1904) R
SpearmanMulti Spearman Correlations Over Multiple Data Sets and a Single Sample Set (Useful for Multi-Omics) Python
SpearmanTies Spearman, and Can Handle Rank Ties R
SpearmanTiesMulti Hybrid Functionality of SpearmanTies and SpearmanMulti Python
SPIECEASI SPIEC-EASI (Kurtz et al, 2015) R
Centrality
Name Short Description Language
ATria Ablatio Triadum (ATria) Centrality (Cickovski et al, 2017) C++
BiasedPageRank Edge-Weighted Personalized Page Rank (Xie et al, 2015) Python
Conquests Conquests algorithm (Laniau et al, 2017) for Phenotypically Essential Metabolites Python
Degree Degree Centrality (Freeman, 1979) C++
Exponential Exponential Centality (Benzi and Klymko, 2013) Python
GPUATria GPUATria (ATria, on the GPU) CUDA
Katz Katz Prestige Centrality (Katz, 1953) C++
MATria Multiple Ablatio Triadium (Cickovski et al, 2017) Python
NetCooperate NetCooperate Algorithm for Key Metabolites (Levy et al, 2015) Python
PageRank Page Rank Centrality (Page, 1999) Python
PyATria ATria, in Python Python
Clustering
Name Short Description Language
AffinityPropagation Affinity Propagation (Frey and Dueck, 2007) Python
CKMeans CKMeans (Wang and Song, 2011) R
Louvain Louvain Clustering (Blondel et al, 2008) Python
MCL Markov Clustering (van Dongen, 2000) R
ModularityMaximization Modularity Maximization Algorithm For Clustering Level Python
SIMLR SIMLR (Wang et al, 2017) R
Spectral Spectral Clustering (Meila and Shi, 2001) Python
Time Series
Name Short Description Language
AutoCorrelation Autocorrelation Function Estimate R
CCM Convergent Cross Mapping (Sugihara et al, 2012) R
CrossCorrelation Time-Series Cross-Correlation Values R
Detrend Detrend (Least-Squares Fit, Time Series Data) R
DickeyFuller Dickey-Fuller Test, Time Series Data (Said and Dickey, 1984) R
Granger Granger Causality (Granger, 1969) R
External Tools
Name Short Description Language
MetaBAT MetaBAT (Kang et al, 2015) (Generated by PluGen) C++
Mothur Mothur (Schloss, 2009) (Generated by PluGen) C++
Miscellaneous
Name Short Description Language
Classify Phylogenetic OTU Classifier Python
MakeCliques Make a Network of Cliques (Python) Python
MakeSynthetic Make a Synthetic Network Python
NorTA Normal-To-Anything algorithm R

 

 

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