Cargando…

RNA splicing analysis using heterogeneous and large RNA-seq datasets

The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit inc...

Descripción completa

Detalles Bibliográficos
Autores principales:	Vaquero-Garcia, Jorge, Aicher, Joseph K., Jewell, San, Gazzara, Matthew R., Radens, Caleb M., Jha, Anupama, Norton, Scott S., Lahens, Nicholas F., Grant, Gregory R., Barash, Yoseph
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2023
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9984406/ https://www.ncbi.nlm.nih.gov/pubmed/36869033 http://dx.doi.org/10.1038/s41467-023-36585-y

Ejemplares similares

MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis
por: Slaff, Barry, et al.
Publicado: (2021)

Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study
por: Jha, Anupama, et al.
Publicado: (2020)

Integrative deep models for alternative splicing
por: Jha, Anupama, et al.
Publicado: (2017)

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

Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing
por: Radens, Caleb M., et al.
Publicado: (2020)

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
por: Gazzara, Matthew R., et al.
Publicado: (2017)

A new view of transcriptome complexity and regulation through the lens of local splicing variations
por: Vaquero-Garcia, Jorge, et al.
Publicado: (2016)

Alternative splicing of apoptosis genes promotes human T cell survival
por: Blake, Davia, et al.
Publicado: (2022)

A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers
por: Wang, David, et al.
Publicado: (2023)

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
por: Hayer, Katharina E., et al.
Publicado: (2015)

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing
por: Agosto, Laura M., et al.
Publicado: (2019)

SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets
por: Li, Jin, et al.
Publicado: (2017)

Integrated analysis of a compendium of RNA-Seq datasets for splicing factors
por: Yu, Peng, et al.
Publicado: (2020)

An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning
por: Ehrmann, Ingrid, et al.
Publicado: (2019)

Fugacium Spliced Leader Genes Identified from Stranded RNA-Seq Datasets
por: Song, Yue, et al.
Publicado: (2019)

Comparative evaluation of full-length isoform quantification from RNA-Seq
por: Sarantopoulou, Dimitra, et al.
Publicado: (2021)

Joint analysis of heterogeneous single-cell RNA-seq dataset collections
por: Barkas, Nikolas, et al.
Publicado: (2019)

GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure
por: Hadish, John A., et al.
Publicado: (2022)

CAMPAREE: a robust and configurable RNA expression simulator
por: Lahens, Nicholas F., et al.
Publicado: (2021)

Publisher Correction: Integrated analysis of a compendium of RNA-Seq datasets for splicing factors
por: Yu, Peng, et al.
Publicado: (2020)

Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins
por: Capitanchik, Charlotte, et al.
Publicado: (2018)

Supersplat—spliced RNA-seq alignment
por: Bryant, Douglas W., et al.
Publicado: (2010)

Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation
por: Martinez, Nicole M., et al.
Publicado: (2015)

Systematic evaluation of spliced alignment programs for RNA-seq data
por: Engström, Pär G, et al.
Publicado: (2013)

POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching
por: Holmström, Susanna, et al.
Publicado: (2022)

IVT-seq reveals extreme bias in RNA sequencing
por: Lahens, Nicholas F, et al.
Publicado: (2014)

BEERS2: RNA-Seq simulation through high fidelity in silico modeling
por: Brooks, Thomas G., et al.
Publicado: (2023)

ARH-seq: identification of differential splicing in RNA-seq data
por: Rasche, Axel, et al.
Publicado: (2014)

AVISPA: a web tool for the prediction and analysis of alternative splicing
por: Barash, Yoseph, et al.
Publicado: (2013)

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq
por: Hartley, Stephen W., et al.
Publicado: (2016)

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data
por: Bryce-Smith, Sam, et al.
Publicado: (2023)

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data
por: Bryce-Smith, Sam, et al.
Publicado: (2023)

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation
por: Brady, Lauren K., et al.
Publicado: (2017)

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq
por: Hu, Yin, et al.
Publicado: (2013)

Model-based detection of alternative splicing signals
por: Barash, Yoseph, et al.
Publicado: (2010)

TopHat: discovering splice junctions with RNA-Seq
por: Trapnell, Cole, et al.
Publicado: (2009)

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)

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
por: Wang, Kai, et al.
Publicado: (2010)

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
por: LeGault, Laura H., et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_2u6rkldforh486ab2bvm3u1epr