Cargando…

ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences

BACKGROUND: High-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological...

Descripción completa

Detalles Bibliográficos
Autores principales:	Catlett, Dylan, Son, Kevin, Liang, Connie
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2021
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8320524/ https://www.ncbi.nlm.nih.gov/pubmed/34395092 http://dx.doi.org/10.7717/peerj.11865

Ejemplares similares

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
por: Redelings, Benjamin D., et al.
Publicado: (2017)

Ensemble learning for detecting gene-gene interactions in colorectal cancer
por: Dorani, Faramarz, et al.
Publicado: (2018)

SMARTAR: an R package for designing and analyzing Sequential Multiple Assignment Randomized Trials
por: Zhong, Xiaobo, et al.
Publicado: (2021)

Ensembl Genomes: Extending Ensembl across the taxonomic space
por: Kersey, P. J., et al.
Publicado: (2010)

Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments
por: Lydon, Keri Ann, et al.
Publicado: (2018)

Ensemble of adapted convolutional neural networks (CNN) methods for classifying colon histopathological images
por: Albashish, Dheeb
Publicado: (2022)

ECOVNet: a highly effective ensemble based deep learning model for detecting COVID-19
por: Chowdhury, Nihad Karim, et al.
Publicado: (2021)

Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers
por: Yu, Xin, et al.
Publicado: (2021)

An ensemble machine learning model based on multiple filtering and supervised attribute clustering algorithm for classifying cancer samples
por: Bose, Shilpi, et al.
Publicado: (2021)

A multi-kernel and multi-scale learning based deep ensemble model for predicting recurrence of non-small cell lung cancer
por: Kim, Gihyeon, et al.
Publicado: (2023)

SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction
por: Yan, Wu, et al.
Publicado: (2023)

An R package for ensemble learning stacking
por: Nukui, Taichi, et al.
Publicado: (2023)

phydms: software for phylogenetic analyses informed by deep mutational scanning
por: Hilton, Sarah K., et al.
Publicado: (2017)

BLAST-based validation of metagenomic sequence assignments
por: Bazinet, Adam L., et al.
Publicado: (2018)

Plastome phylogenomics and characterization of rare genomic changes as taxonomic markers in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)
por: Orton, Lauren M., et al.
Publicado: (2019)

Assigning confidence scores to homoeologs using fuzzy logic
por: Glover, Natasha M., et al.
Publicado: (2019)

Ensemble Estimation of Information Divergence †
por: Moon, Kevin R., et al.
Publicado: (2018)

Assessing alignment-based taxonomic classification of ancient microbial DNA
por: Eisenhofer, Raphael, et al.
Publicado: (2019)

Taxonomic evaluation of selected Ganoderma species and database sequence validation
por: Jargalmaa, Suldbold, et al.
Publicado: (2017)

Spatiotemporal Clustering of Repeated Super-Resolution Localizations via Linear Assignment Problem
por: Schodt, David J., et al.
Publicado: (2021)

Mutational signature assignment heterogeneity is widespread and can be addressed by ensemble approaches
por: Wu, Andy J, et al.
Publicado: (2023)

A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use
por: Reginato, Marcelo
Publicado: (2022)

Corrigendum: Spatiotemporal Clustering of Repeated Super-Resolution Localizations via Linear Assignment Problem
por: Schodt, David J., et al.
Publicado: (2022)

Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data
por: DeMario, Samuel, et al.
Publicado: (2023)

MTSv: rapid alignment-based taxonomic classification and high-confidence metagenomic analysis
por: Furstenau, Tara N., et al.
Publicado: (2022)

EcoCountHelper: an R package and analytical pipeline for the analysis of ecological count data using GLMMs, and a case study of bats in Grand Teton National Park
por: Cole, Hunter J., et al.
Publicado: (2022)

Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
por: Cho, Yoonhee, et al.
Publicado: (2021)

intansv: an R package for integrative analysis of structural variations
por: Jia, Lihua, et al.
Publicado: (2020)

Imputing missing distances in molecular phylogenetics
por: Xia, Xuhua
Publicado: (2018)

Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array
por: Zhang, Xu, et al.
Publicado: (2014)

Sicegar: R package for sigmoidal and double-sigmoidal curve fitting
por: Caglar, M. Umut, et al.
Publicado: (2018)

The seeker R package: simplified fetching and processing of transcriptome data
por: Schoenbachler, Joshua L., et al.
Publicado: (2022)

GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data
por: Tataru, Christine, et al.
Publicado: (2022)

Ensembl BioMarts: a hub for data retrieval across taxonomic space
por: Kinsella, Rhoda J., et al.
Publicado: (2011)

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes
por: Gregor, Ivan, et al.
Publicado: (2016)

Probabilistic Ensemble of Deep Information Networks
por: Franzese, Giulio, et al.
Publicado: (2020)

PhyloSift: phylogenetic analysis of genomes and metagenomes
por: Darling, Aaron E., et al.
Publicado: (2014)

phylopath: Easy phylogenetic path analysis in R
por: van der Bijl, Wouter
Publicado: (2018)

Iroki: automatic customization and visualization of phylogenetic trees
por: Moore, Ryan M., et al.
Publicado: (2020)

Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem
por: Mohammadi, Sara, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_552g580janjvjpn9aj1pc81ka1