movingpictures83/Network

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Language
R
License
MIT License
Created over 4 years ago
Updated almost 3 years ago

movingpictures83/Network

movingpictures83

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PluMA plugin to plot samples as a network, with edge weights representing dissimilarity

MWM

PluMA plugin to run the maximum weighted matching algorithm (Galil, 1986)

PLSDA-Multiple

Run PLS-DA on multiple datasets

Prank

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 filter

KronaNoVirus

Remove viruses from Krona file

BioNet

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 Data

PLSDA

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 metabolites

AssemblyStats

Output statistics on any number of full genome assemblies

LMSStar

A repository of scripts for interfacing to and converting between popular learning management systems, including ZyBooks, Gradescope, and Canvas.

Clusterize

PluMA plugin to remove edges between nodes in different clusters of a network

SPIECEASI

PluMA plugin for SPIEC-EASI (Kurtz et al 2015)

CountTableProcessing

PluMA plugin to convert OTU counts from Mothur into a CSV file of abundances

CCM

PluMA plugin that runs the Convergent Cross Mapping (CCM, Sugihara et al 2012) algorithm for detecting causality

SPLSDA

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 2018

TriadCounter

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)