Cargando…

Learning sparse log-ratios for high-throughput sequencing data

MOTIVATION: The automatic discovery of sparse biomarkers that are associated with an outcome of interest is a central goal of bioinformatics. In the context of high-throughput sequencing (HTS) data, and compositional data (CoDa) more generally, an important class of biomarkers are the log-ratios bet...

Descripción completa

Detalles Bibliográficos
Autores principales:	Gordon-Rodriguez, Elliott, Quinn, Thomas P, Cunningham, John P
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Original Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8696089/ https://www.ncbi.nlm.nih.gov/pubmed/34498030 http://dx.doi.org/10.1093/bioinformatics/btab645

Ejemplares similares

The limits of log-ratios
por: Sharov, Vasily, et al.
Publicado: (2004)

Super-sparse principal component analyses for high-throughput genomic data
por: Lee, Donghwan, et al.
Publicado: (2010)

Error Propagation in Isometric Log-ratio Coordinates for Compositional Data: Theoretical and Practical Considerations
por: Mert, Mehmet Can, et al.
Publicado: (2016)

A zero inflated log-normal model for inference of sparse microbial association networks
por: Prost, Vincent, et al.
Publicado: (2021)

Performance of Firth-and logF-type penalized methods in risk prediction for small or sparse binary data
por: Rahman, M. Shafiqur, et al.
Publicado: (2017)

High dimensional model representation of log likelihood ratio: binary classification with SNP data
por: pour, Ali Foroughi, et al.
Publicado: (2020)

High dimensional model representation of log-likelihood ratio: binary classification with expression data
por: Foroughi pour, Ali, et al.
Publicado: (2020)

Development of a high throughput assay for indirectly measuring phage growth using the OmniLog(TM) system
por: Henry, Matthew, et al.
Publicado: (2012)

Population Genomic Inferences from Sparse High-Throughput Sequencing of Two Populations of Drosophila melanogaster
por: Sackton, Timothy B., et al.
Publicado: (2009)

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
por: Quinn, Thomas P., et al.
Publicado: (2018)

Exploring generative deep learning for omics data using log-linear models
por: Hess, Moritz, et al.
Publicado: (2020)

High-Throughput Mass Spectrometry Imaging with Dynamic Sparse Sampling
por: Hu, Hang, et al.
Publicado: (2022)

Improved analysis of bacterial CGH data beyond the log-ratio paradigm
por: Snipen, Lars, et al.
Publicado: (2009)

Active learning for efficient analysis of high-throughput nanopore data
por: Guan, Xiaoyu, et al.
Publicado: (2022)

PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data
por: Hao, Jie, et al.
Publicado: (2018)

Compression of Structured High-Throughput Sequencing Data
por: Campagne, Fabien, et al.
Publicado: (2013)

Counts: an outstanding challenge for log-ratio analysis of compositional data in the molecular biosciences
por: Lovell, David R, et al.
Publicado: (2020)

Log‐ratio analysis of microbiome data with many zeroes is library size dependent
por: te Beest, Dennis E., et al.
Publicado: (2021)

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
por: Althammer, Sonja, et al.
Publicado: (2011)

Data-based filtering for replicated high-throughput transcriptome sequencing experiments
por: Rau, Andrea, et al.
Publicado: (2013)

HTSeq—a Python framework to work with high-throughput sequencing data
por: Anders, Simon, et al.
Publicado: (2015)

High-throughput sequencing data and the impact of plant gene annotation quality
por: Vaattovaara, Aleksia, et al.
Publicado: (2019)

S-leaping: an efficient downsampling method for large high-throughput sequencing data
por: Kuwahara, Hiroyuki, et al.
Publicado: (2023)

Data logging for technical services at CERN
por: Martini, R, et al.
Publicado: (1995)

Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines
por: Macdonald, John M., et al.
Publicado: (2016)

Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data
por: Zhu, Sha Joe, et al.
Publicado: (2018)

Normalization by distributional resampling of high throughput single-cell RNA-sequencing data
por: Brown, Jared, et al.
Publicado: (2021)

A method of back-calculating the log odds ratio and standard error of the log odds ratio from the reported group-level risk of disease
por: Hu, Dapeng, et al.
Publicado: (2020)

Detecting genomic deletions from high-throughput sequence data with unsupervised learning
por: Li, Xin, et al.
Publicado: (2023)

Determination of crystallographic intensities from sparse data
por: Ayyer, Kartik, et al.
Publicado: (2015)

Interpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance Selection
por: Quinn, Thomas P., et al.
Publicado: (2020)

SAMQA: error classification and validation of high-throughput sequenced read data
por: Robinson, Thomas, et al.
Publicado: (2011)

Log In to Experiential Learning Theory: Supporting Web-Based Faculty Development
por: Omer, Selma, et al.
Publicado: (2017)

Bias in Odds Ratios From Logistic Regression Methods With Sparse Data Sets
por: Gosho, Masahiko, et al.
Publicado: (2023)

Cloud Log Data Analysis
por: Oak, Shweta
Publicado: (2017)

Logging of Supervisory Data at BESSY
por: Birke, T, et al.
Publicado: (1999)

Log Data Analysis with R
por: DUELLMANN, Dirk
Publicado: (2014)

Deep learning for photoacoustic tomography from sparse data
por: Antholzer, Stephan, et al.
Publicado: (2018)

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
por: Carver, Tim, et al.
Publicado: (2012)

Genome reassembly with high-throughput sequencing data
por: Parrish, Nathaniel, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_o5naers021op8lhei618tq4n8q