Cargando…

SplicePlot: a utility for visualizing splicing quantitative trait loci

Summary: RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wu, Eric, Nance, Tracy, Montgomery, Stephen B.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967110/ https://www.ncbi.nlm.nih.gov/pubmed/24363378 http://dx.doi.org/10.1093/bioinformatics/btt733

Ejemplares similares

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
por: Ryan, Michael C., et al.
Publicado: (2012)

Jutils: a visualization toolkit for differential alternative splicing events
por: Yang, Guangyu, et al.
Publicado: (2021)

FlexDotPlot: a universal and modular dot plot visualization tool for complex multifaceted data
por: Leonard, Simon, et al.
Publicado: (2022)

pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS
por: Scherer, Nora, et al.
Publicado: (2021)

genoPlotR: comparative gene and genome visualization in R
por: Guy, Lionel, et al.
Publicado: (2010)

CoMut: visualizing integrated molecular information with comutation plots
por: Crowdis, Jett, et al.
Publicado: (2020)

mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
por: Movassagh, Mercedeh, et al.
Publicado: (2023)

PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data
por: Tokheim, Collin, et al.
Publicado: (2014)

BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms
por: Sosnowski, Olivier, et al.
Publicado: (2012)

Flashfm-ivis: interactive visualization for fine-mapping of multiple quantitative traits
por: Zhou, Feng, et al.
Publicado: (2022)

Mapping Splicing Quantitative Trait Loci in RNA-Seq
por: Jia, Cheng, et al.
Publicado: (2014)

Mapping Splicing Quantitative Trait Loci in RNA-Seq
por: Jia, Cheng, et al.
Publicado: (2015)

Investigation of Splicing Quantitative Trait Loci in Arabidopsis thaliana
por: Yoo, Wonseok, et al.
Publicado: (2016)

DIEGO: detection of differential alternative splicing using Aitchison’s geometry
por: Doose, Gero, et al.
Publicado: (2018)

Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype
por: Watkinson, John, et al.
Publicado: (2009)

ConPlot: web-based application for the visualization of protein contact maps integrated with other data
por: Sánchez Rodríguez, Filomeno, et al.
Publicado: (2021)

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications
por: Laird, Matthew R., et al.
Publicado: (2015)

Intron-centric estimation of alternative splicing from RNA-seq data
por: Pervouchine, Dmitri D., et al.
Publicado: (2013)

ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping
por: Lou, Shao-Ke, et al.
Publicado: (2011)

CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs
por: Wu, Jing, et al.
Publicado: (2019)

Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples
por: Wilks, Christopher, et al.
Publicado: (2018)

EcoPLOT: dynamic analysis of biogeochemical data
por: Sanchez, Christopher D, et al.
Publicado: (2021)

CBNplot: Bayesian network plots for enrichment analysis
por: Sato, Noriaki, et al.
Publicado: (2022)

AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts
por: Shionyu, Masafumi, et al.
Publicado: (2012)

MADS+: discovery of differential splicing events from Affymetrix exon junction array data
por: Shen, Shihao, et al.
Publicado: (2010)

TSIS: an R package to infer alternative splicing isoform switches for time-series data
por: Guo, Wenbin, et al.
Publicado: (2017)

SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion
por: Canson, Daffodil M, et al.
Publicado: (2023)

r2cat: synteny plots and comparative assembly
por: Husemann, Peter, et al.
Publicado: (2010)

TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts
por: Wyman, Dana, et al.
Publicado: (2019)

pyGenomeTracks: reproducible plots for multivariate genomic datasets
por: Lopez-Delisle, Lucille, et al.
Publicado: (2020)

ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins
por: Mall, Tarun, et al.
Publicado: (2016)

MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data
por: Green, Christopher J, et al.
Publicado: (2018)

EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics
por: Arora, Chakit, et al.
Publicado: (2023)

FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing
por: Liu, Jinding, et al.
Publicado: (2023)

PyOncoPrint: a python package for plotting OncoPrints
por: Park, Jeongbin, et al.
Publicado: (2023)

FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci
por: Rambaldi, Davide, et al.
Publicado: (2009)

ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci
por: Zhang, Tongwu, et al.
Publicado: (2022)

forqs: forward-in-time simulation of recombination, quantitative traits and selection
por: Kessner, Darren, et al.
Publicado: (2014)

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
por: Gel, Bernat, et al.
Publicado: (2017)

A compendium of uniformly processed human gene expression and splicing quantitative trait loci
por: Kerimov, Nurlan, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_b4vrhhoor03kncarortki69q3v