Browse the PluMA plugin pool

Full genome assembly statistics (Generated by PluGen)

Assess gene assembly and/or annotation using BUSCO (Simao et al, 2015)

Burrows-Wheeler Alignment (Li and Durbin, 2009)

Canu (Koren et al, 2017) long-read genome assembly (Generated by PluGen)

Circlator (Hunt et al, 2015) genome circularization (Generated by PluGen)

Linearize a circular DNA sequence

Flye genome assembly with long reads (Kolmogorov et al, 2019)

Iterative De Brujin genome Assembler (Peng et al, 2012) (Generated by PluGen)

KMerGenie optimal k-mer length for assembly (Chikhi and Medvedev, 2014)

MEDUSA (Bosi et al, 2015) genome scaffolding (Generated by PluGen)

MegaHit (Li et al, 2015) genome assembly (Generated by PluGen)

Metagenome assembly evaluation using MetaQuast (Mikheenko et al, 2016)

PluMA plugin to run MetaSPAdes (Nurk et al, 2017) genome assembler (Generated by PluGen)

Quality Assessment Tool for Genome Assemblies (Gurevich et al, 2013)

Change position of a set of genes based on a reference gene

SeqPrep (St. John, 2016)

SKESA (Souvorov et al, 2018) genome assembly (Generated by PluGen)

SPAdes (Bankevich et al, 2012) genome assembly (Generated by PluGen)

Unicycler genome assembly (Wick et al, 2017) (Generated by PluGen).

Velvet (Zerbino and Birney, 2008) de Novo Assembly

XORRO (Dickson and Gloor, 2013)

Analysis Of Differential Abundance Taking Sample Variation Into Account (Fernandes et al, 2013)

Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC, Lin et al 2020)

Count Regression for Correlated Observations with the Beta-binomial (CORNCOB) (Martin et al, 2020)

Robust differential expression analysis

Differential Gene Expression Analysis Based on the Negative Binomial Distribution (Love et al, 2014)

Fast Minimum Redundancy Maximum algorithm (Ramirez-Gallegos et al, 2016) for feature selection (Generated by PluGen)

Determine the most distinguishing features for case vs control

Find marker genes (RNA)

HMMER (Finn et al, 2011) (Generated by PluGen)

Linear discriminant analysis Effect Size (LEfSe) (Segata et al, 2011)

Limma (Ritchie et al, 2015)

Multiple Testing of Taxa Abundances According to Sample Category (McMurdie, 2020)

Compute pS219/total alpha-synulein ratio (Lewy-body biomarker)

Wald test for statistical hypothesis (Wald, 1943)

Adaptive Learning Cache Replacement (Yusuf et al, 2021)

Adaptive Replacement Cache

BANDIT replacement (Sridharan et al, 2020)

Cache Nucleus (Omniverse, 2021)

Statistics on caches

Synthetic dataset for cache

Synthetic dataset for cache, adaptive

Cacheus test (Rodriguez et al, 2021)

Cache visualization

Dynamic Low Inter-reference Recency Set (Li et al, 2018)

Epsilon distribution

Exponential distribution

Expert Learning

FAR (Vietri et al, 2018)

Graph Document Object Model

Hyperbolic Adaptive Learning Cache Replacement (Yusuf et al, 2022)

Heatmap, restricted to top 5%

Average hit rate

LaCReMA2 replacement

LaCReME replacement

Learning Cache Replacement (Jiang et al, 2002)

Least-Frequently Used Replacement

Low Inter-reference Recency Set (Jiang et al, 2002)

LOMP cache replacement

Learning rate plot