Cargando…

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

BACKGROUND: Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wan, Yu, Wick, Ryan R., Zobel, Justin, Ingle, Danielle J., Inouye, Michael, Holt, Kathryn E.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2020
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513276/ https://www.ncbi.nlm.nih.gov/pubmed/32972363 http://dx.doi.org/10.1186/s12864-020-07019-6

Ejemplares similares

SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees
por: Hill, Tobias, et al.
Publicado: (2010)

Short read sequence typing (SRST): multi-locus sequence types from short reads
por: Inouye, Michael, et al.
Publicado: (2012)

HGT-Gen: a tool for generating a phylogenetic tree with horizontal gene transfer
por: Horiike, Tokumasa, et al.
Publicado: (2011)

geneHapR: an R package for gene haplotypic statistics and visualization
por: Zhang, Renliang, et al.
Publicado: (2023)

EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes
por: Clasen, Frederick Johannes, et al.
Publicado: (2018)

geneHummus: an R package to define gene families and their expression in legumes and beyond
por: Die, Jose V., et al.
Publicado: (2019)

GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials
por: Zhao, Yingdong, et al.
Publicado: (2015)

Mycelia as a focal point for horizontal gene transfer among soil bacteria
por: Berthold, Tom, et al.
Publicado: (2016)

GSAR: Bioconductor package for Gene Set analysis in R
por: Rahmatallah, Yasir, et al.
Publicado: (2017)

xcore: an R package for inference of gene expression regulators
por: Migdał, Maciej, et al.
Publicado: (2023)

The chromosomal organization of horizontal gene transfer in bacteria
por: Oliveira, Pedro H., et al.
Publicado: (2017)

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
por: Inouye, Michael, et al.
Publicado: (2014)

SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction
por: Abraham, Gad, et al.
Publicado: (2012)

graphite - a Bioconductor package to convert pathway topology to gene network
por: Sales, Gabriele, et al.
Publicado: (2012)

ORdensity: user-friendly R package to identify differentially expressed genes
por: Martínez-Otzeta, José María, et al.
Publicado: (2020)

rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms
por: Sayols, Sergi
Publicado: (2023)

Horizontal functional gene transfer from bacteria to fishes
por: Sun, Bao-Fa, et al.
Publicado: (2015)

Chromosome architecture constrains horizontal gene transfer in bacteria
por: Hendrickson, Heather L., et al.
Publicado: (2018)

Extensive horizontal gene transfer in cheese-associated bacteria
por: Bonham, Kevin S, et al.
Publicado: (2017)

Horizontal gene transfer drives the evolution of dependencies in bacteria
por: Goyal, Akshit
Publicado: (2022)

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
por: Rue-Albrecht, Kévin, et al.
Publicado: (2016)

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips
por: Turro, Ernest, et al.
Publicado: (2007)

ICGE: an R package for detecting relevant clusters and atypical units in gene expression
por: Irigoien, Itziar, et al.
Publicado: (2012)

svapls: an R package to correct for hidden factors of variability in gene expression studies
por: Chakraborty, Sutirtha, et al.
Publicado: (2013)

DepthTools: an R package for a robust analysis of gene expression data
por: Torrente, Aurora, et al.
Publicado: (2013)

mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics
por: Sakellariou, Argiris, et al.
Publicado: (2015)

iGC—an integrated analysis package of gene expression and copy number alteration
por: Lai, Yi-Pin, et al.
Publicado: (2017)

GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
por: Marini, Federico, et al.
Publicado: (2021)

The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
por: Ben Guebila, Marouen, et al.
Publicado: (2023)

Horizontal Gene Transfer
por: Burmeister, Alita R.
Publicado: (2015)

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae
por: Wyres, Kelly L., et al.
Publicado: (2019)

sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters
por: Tripathi, Shailesh, et al.
Publicado: (2017)

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon
por: Makkay, Andrea M., et al.
Publicado: (2020)

GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest
por: Diaz-Uriarte, Ramón
Publicado: (2007)

FUNC: a package for detecting significant associations between gene sets and ontological annotations
por: Prüfer, Kay, et al.
Publicado: (2007)

DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data
por: Glez-Peña, Daniel, et al.
Publicado: (2009)

iGTP: A software package for large-scale gene tree parsimony analysis
por: Chaudhary, Ruchi, et al.
Publicado: (2010)

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference
por: Bellot, Pau, et al.
Publicado: (2015)

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
por: Stamm, Karl, et al.
Publicado: (2019)

Effect of the environment on horizontal gene transfer between bacteria and archaea
por: Fuchsman, Clara A., et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_sioi20b31fv08bm9qr6v7tq5c2