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  • Language
    Shell
  • License
    MIT License
  • Created almost 5 years ago
  • Updated almost 4 years ago

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Repository Details

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

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1

Network

PluMA plugin to plot samples as a network, with edge weights representing dissimilarity
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2

MWM

PluMA plugin to run the maximum weighted matching algorithm (Galil, 1986)
Python
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3

PLSDA-Multiple

Run PLS-DA on multiple datasets
R
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4

Prank

Perform multiple sequence alignment with Prank (Loytynoja, 2014)
C++
1
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5

GMM

Gaussian Mixture Model clustering (Rasmussen, 1999)
R
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6

Tightness

Determine the tightness of a set of clusters in a network by calculating means and standard deviations of their edge weights.
R
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7

GPUBisection

GPU Bisection Method (Jardines et al, 2016)
C++
1
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8

FASTQFilter

Remove sequences from a FASTQ file, using a SAM filter
Python
1
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9

KronaNoVirus

Remove viruses from Krona file
Python
1
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10

BioNet

A generic network class for biology.
C++
1
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11

HMM

Hidden Markov Model clustering (Lin and Li, 2017)
R
1
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12

DickeyFuller

PluMA plugin that runs the Dickey-Fuller Test (Said and Dickey, 1984) for Time-Series Data
R
1
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13

PLSDA

PluMA plugin that runs Partial Least Squares Discriminant Analysis (PLS-DA, Stahle and Wold 1987)
R
1
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14

Tax4Fun2LEfSe

Convert Tax4Fun2 (Wemheuer et al, 2020) output to LEfSe input format (Segata et al, 2011)
Python
1
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15

Conquests

Conquests algorithm (Laniau et al, 2017) for phenotypically essential metabolites
Python
1
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16

AssemblyStats

Output statistics on any number of full genome assemblies
C++
1
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17

Clusterize

PluMA plugin to remove edges between nodes in different clusters of a network
Python
1
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18

SPIECEASI

PluMA plugin for SPIEC-EASI (Kurtz et al 2015)
R
1
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19

CountTableProcessing

PluMA plugin to convert OTU counts from Mothur into a CSV file of abundances
R
1
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20

CCM

PluMA plugin that runs the Convergent Cross Mapping (CCM, Sugihara et al 2012) algorithm for detecting causality
R
1
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21

SPLSDA

Sparse Partial Least Squares Differential Analysis (SPLSDA) (LeCao et al, 2011)
R
1
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22

RWRMH

PluMA plugin that runs Random Walk with Restart on Multiplex and Heterogeneous biological networks (Valdeolivas et al, 2018)
R
1
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23

SpearmanTies

Computes Spearman correlations and handles ties.
Python
1
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24

Farelogix

Examples From C++ Course in Summer 2018
HTML
1
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25

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)
Python
1
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