Cargando…

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage

BACKGROUND: RNA-seq has been a boon to the quantitative analysis of transcriptomes. A notable application is the detection of changes in transcript usage between experimental conditions. For example, discovery of pathological alternative splicing may allow the development of new treatments or better...

Descripción completa

Detalles Bibliográficos
Autores principales:	Soneson, Charlotte, Matthes, Katarina L., Nowicka, Malgorzata, Law, Charity W., Robinson, Mark D.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2016
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729156/ https://www.ncbi.nlm.nih.gov/pubmed/26813113 http://dx.doi.org/10.1186/s13059-015-0862-3

Ejemplares similares

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
por: Van den Berge, Koen, et al.
Publicado: (2017)

On-Line Prefiltering and Improved Data Collection on LSD
por: Ghesquière, Claude
Publicado: (1972)

Prefiltering Model for Homology Detection Algorithms on GPU
por: Retamosa, Germán, et al.
Publicado: (2016)

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
por: Love, Michael I., et al.
Publicado: (2018)

Characterizations of Some Fuzzy Prefilters (Filters) in EQ-Algebras
por: Xin, Xiao Long, et al.
Publicado: (2014)

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
por: Weber, Lukas M., et al.
Publicado: (2019)

A Mathematical Investigation into the Design of Prefilters That Make Cameras More Colorimetric †
por: Zhu, Yuteng, et al.
Publicado: (2020)

Statistical methods for detecting differentially methylated loci and regions
por: Robinson, Mark D., et al.
Publicado: (2014)

A Prefiltered Cuckoo Search Algorithm with Geometric Operators for Solving Sudoku Problems
por: Soto, Ricardo, et al.
Publicado: (2014)

Prefiltering based on experimental paradigm for analysis of fMRI complex brain networks
por: Jiménez, Salvador, et al.
Publicado: (2020)

Towards unified quality verification of synthetic count data with countsimQC
por: Soneson, Charlotte, et al.
Publicado: (2018)

Leak Detection and Location of Water Pipes Using Vibration Sensors and Modified ML Prefilter
por: Choi, Jihoon, et al.
Publicado: (2017)

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish
por: Aanes, Håvard, et al.
Publicado: (2013)

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
por: Soneson, Charlotte, et al.
Publicado: (2016)

Using equivalence class counts for fast and accurate testing of differential transcript usage
por: Cmero, Marek, et al.
Publicado: (2019)

A Simplified Baseband Prefilter Model with Adaptive Kalman Filter for Ultra-Tight COMPASS/INS Integration
por: Luo, Yong, et al.
Publicado: (2012)

Prefiltered Single-Carrier Frequency-Domain Equalization for Binary CPM over Shallow Water Acoustic Channel
por: Han, Ruigang, et al.
Publicado: (2022)

Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments
por: Darvish, Mitra, et al.
Publicado: (2022)

A systematic performance evaluation of clustering methods for single-cell RNA-seq data
por: Duò, Angelo, et al.
Publicado: (2020)

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
por: Nowicka, Malgorzata, et al.
Publicado: (2016)

A comparison of methods for differential expression analysis of RNA-seq data
por: Soneson, Charlotte, et al.
Publicado: (2013)

Using machine learning to detect the differential usage of novel gene isoforms
por: Zhang, Xiaopu, et al.
Publicado: (2022)

EBV-regulated global changes in mRNA isoform usage
por: Homa, Nicholas, et al.
Publicado: (2012)

Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes
por: Newman, Jeremy R. B., et al.
Publicado: (2023)

Differential transcript usage in the Parkinson’s disease brain
por: Dick, Fiona, et al.
Publicado: (2020)

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?
por: Zhou, Xiaobei, et al.
Publicado: (2015)

IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data
por: Niu, Liang, et al.
Publicado: (2014)

Detecting differential transcript usage in complex diseases with SPIT
por: Erdogdu, Beril, et al.
Publicado: (2023)

Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68
por: O’Grady, Tina, et al.
Publicado: (2019)

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
por: Orjuela, Stephany, et al.
Publicado: (2019)

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
por: Soneson, Charlotte, et al.
Publicado: (2019)

SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples
por: Kimes, Patrick K., et al.
Publicado: (2014)

Tissue-specific developmental regulation and isoform usage underlie the role of doublesex in sex differentiation and mimicry in Papilio swallowtails
por: Deshmukh, Riddhi, et al.
Publicado: (2020)

voom: precision weights unlock linear model analysis tools for RNA-seq read counts
por: Law, Charity W, et al.
Publicado: (2014)

Batch Effect Confounding Leads to Strong Bias in Performance Estimates Obtained by Cross-Validation
por: Soneson, Charlotte, et al.
Publicado: (2014)

Kalrn promoter usage and isoform expression respond to chronic cocaine exposure
por: Mains, Richard E, et al.
Publicado: (2011)

Aberrant DNA methylation defines isoform usage in cancer, with functional implications
por: Chen, Yun-Ching, et al.
Publicado: (2019)

Alternative Splicing Isoforms of Porcine CREB Are Differentially Involved in Transcriptional Transactivation
por: Zhang, Dongjie, et al.
Publicado: (2022)

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes
por: Tiberi, Simone, et al.
Publicado: (2023)

Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer
por: Liu, Jinfeng, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_npoft14qskv9v0a0jpci7l2hes