movingpictures83/Prank movingpictures83/Prank

  • Stars
    star
    1
  • Language
    C++
  • License
    MIT License
  • Created almost 3 years ago
  • Updated about 2 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
movingpictures83/Prank
github

movingpictures83

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Perform multiple sequence alignment with Prank (Loytynoja, 2014)

More Repositories

1

Network

PluMA plugin to plot samples as a network, with edge weights representing dissimilarity
R
1
star
2

MWM

PluMA plugin to run the maximum weighted matching algorithm (Galil, 1986)
Python
1
star
3

PLSDA-Multiple

Run PLS-DA on multiple datasets
R
1
star
4

GMM

Gaussian Mixture Model clustering (Rasmussen, 1999)
R
1
star
5

Tightness

Determine the tightness of a set of clusters in a network by calculating means and standard deviations of their edge weights.
R
1
star
6

GPUBisection

GPU Bisection Method (Jardines et al, 2016)
C++
1
star
7

FASTQFilter

Remove sequences from a FASTQ file, using a SAM filter
Python
1
star
8

KronaNoVirus

Remove viruses from Krona file
Python
1
star
9

BioNet

A generic network class for biology.
C++
1
star
10

HMM

Hidden Markov Model clustering (Lin and Li, 2017)
R
1
star
11

DickeyFuller

PluMA plugin that runs the Dickey-Fuller Test (Said and Dickey, 1984) for Time-Series Data
R
1
star
12

PLSDA

PluMA plugin that runs Partial Least Squares Discriminant Analysis (PLS-DA, Stahle and Wold 1987)
R
1
star
13

Tax4Fun2LEfSe

Convert Tax4Fun2 (Wemheuer et al, 2020) output to LEfSe input format (Segata et al, 2011)
Python
1
star
14

Conquests

Conquests algorithm (Laniau et al, 2017) for phenotypically essential metabolites
Python
1
star
15

AssemblyStats

Output statistics on any number of full genome assemblies
C++
1
star
16

LMSStar

A repository of scripts for interfacing to and converting between popular learning management systems, including ZyBooks, Gradescope, and Canvas.
Shell
1
star
17

Clusterize

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

SPIECEASI

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

CountTableProcessing

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

CCM

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

SPLSDA

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

RWRMH

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

SpearmanTies

Computes Spearman correlations and handles ties.
Python
1
star
24

Farelogix

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