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Network
PluMA plugin to plot samples as a network, with edge weights representing dissimilarityMWM
PluMA plugin to run the maximum weighted matching algorithm (Galil, 1986)PLSDA-Multiple
Run PLS-DA on multiple datasetsPrank
Perform multiple sequence alignment with Prank (Loytynoja, 2014)GMM
Gaussian Mixture Model clustering (Rasmussen, 1999)Tightness
Determine the tightness of a set of clusters in a network by calculating means and standard deviations of their edge weights.GPUBisection
GPU Bisection Method (Jardines et al, 2016)FASTQFilter
Remove sequences from a FASTQ file, using a SAM filterKronaNoVirus
Remove viruses from Krona fileBioNet
A generic network class for biology.HMM
Hidden Markov Model clustering (Lin and Li, 2017)DickeyFuller
PluMA plugin that runs the Dickey-Fuller Test (Said and Dickey, 1984) for Time-Series DataPLSDA
PluMA plugin that runs Partial Least Squares Discriminant Analysis (PLS-DA, Stahle and Wold 1987)Tax4Fun2LEfSe
Convert Tax4Fun2 (Wemheuer et al, 2020) output to LEfSe input format (Segata et al, 2011)Conquests
Conquests algorithm (Laniau et al, 2017) for phenotypically essential metabolitesAssemblyStats
Output statistics on any number of full genome assembliesClusterize
PluMA plugin to remove edges between nodes in different clusters of a networkSPIECEASI
PluMA plugin for SPIEC-EASI (Kurtz et al 2015)CountTableProcessing
PluMA plugin to convert OTU counts from Mothur into a CSV file of abundancesCCM
PluMA plugin that runs the Convergent Cross Mapping (CCM, Sugihara et al 2012) algorithm for detecting causalitySPLSDA
Sparse Partial Least Squares Differential Analysis (SPLSDA) (LeCao et al, 2011)RWRMH
PluMA plugin that runs Random Walk with Restart on Multiplex and Heterogeneous biological networks (Valdeolivas et al, 2018)SpearmanTies
Computes Spearman correlations and handles ties.Farelogix
Examples From C++ Course in Summer 2018TriadCounter
PluMA plugin to take a signed and weighted network and output statistics on the number of triads, including stable and unstable counts (Easley et al, 2010)Love Open Source and this site? Check out how you can help us