Cargando…

A guide to creating design matrices for gene expression experiments

Differential expression analysis of genomic data types, such as RNA-sequencing experiments, use linear models to determine the size and direction of the changes in gene expression. For RNA-sequencing, there are several established software packages for this purpose accompanied with analysis pipeline...

Descripción completa

Detalles Bibliográficos
Autores principales:	Law, Charity W., Zeglinski, Kathleen, Dong, Xueyi, Alhamdoosh, Monther, Smyth, Gordon K., Ritchie, Matthew E.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	F1000 Research Limited 2020
Materias:	Method Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873980/ https://www.ncbi.nlm.nih.gov/pubmed/33604029 http://dx.doi.org/10.12688/f1000research.27893.1

Ejemplares similares

Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
por: You, Yue, et al.
Publicado: (2023)

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
por: Law, Charity W., et al.
Publicado: (2018)

Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
por: You, Yue, et al.
Publicado: (2023)

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods
por: Holik, Aliaksei Z., et al.
Publicado: (2017)

limma powers differential expression analyses for RNA-sequencing and microarray studies
por: Ritchie, Matthew E., et al.
Publicado: (2015)

Easy and efficient ensemble gene set testing with EGSEA
por: Alhamdoosh, Monther, et al.
Publicado: (2017)

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

Consensus clustering approach to group brain connectivity matrices
por: Rasero, Javier, et al.
Publicado: (2017)

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes
por: Oshlack, Alicia, et al.
Publicado: (2007)

Creating 3D visualizations of MRI data: A brief guide
por: Madan, Christopher R.
Publicado: (2015)

Creating small-area deprivation indices: a guide for stages and options
por: Allik, Mirjam, et al.
Publicado: (2020)

P-value-based regulatory motif discovery using positional weight matrices
por: Hartmann, Holger, et al.
Publicado: (2013)

CRISPR‐TAPE: protein‐centric CRISPR guide design for targeted proteome engineering
por: Anderson, Daniel Paolo, et al.
Publicado: (2020)

A Guide for the Design of Evolve and Resequencing Studies
por: Kofler, Robert, et al.
Publicado: (2014)

Gene ontology analysis for RNA-seq: accounting for selection bias
por: Young, Matthew D, et al.
Publicado: (2010)

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing
por: Tian, Luyi, et al.
Publicado: (2021)

Combining multiple tools outperforms individual methods in gene set enrichment analyses
por: Alhamdoosh, Monther, et al.
Publicado: (2017)

MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
por: Doniger, Scott W, et al.
Publicado: (2003)

DeepCRISPR: optimized CRISPR guide RNA design by deep learning
por: Chuai, Guohui, et al.
Publicado: (2018)

Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips
por: Shi, Wei, et al.
Publicado: (2010)

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
por: Chen, Yunshun, et al.
Publicado: (2018)

Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data
por: Cheng, Jinming, et al.
Publicado: (2023)

GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
por: Lee, Da-Inn, et al.
Publicado: (2021)

Missing value imputation using least squares techniques in contaminated matrices
por: Garcia-Peña, Marisol, et al.
Publicado: (2022)

bmlTUX: Design and Control of Experiments in Virtual Reality and Beyond
por: Bebko, Adam O., et al.
Publicado: (2020)

The Assumption of Proportional Components when Candecomp is Applied to Symmetric Matrices in the Context of Indscal
por: Dosse, Mohammed Bennani, et al.
Publicado: (2008)

Comparing cellular bone matrices for posterolateral spinal fusion in a rat model
por: Lin, Cliff, et al.
Publicado: (2020)

The importance of study design for detecting differentially abundant features in high-throughput experiments
por: Luo, Huaien, et al.
Publicado: (2014)

Expression of CRISPR/Cas single guide RNAs using small tRNA promoters
por: Mefferd, Adam L., et al.
Publicado: (2015)

So, you want to create a frog cell line? A guide to establishing frog skin cell lines from tissue explants
por: Bui-Marinos, Maxwell P., et al.
Publicado: (2022)

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses
por: Liu, Ruijie, et al.
Publicado: (2015)

Camera: a competitive gene set test accounting for inter-gene correlation
por: Wu, Di, et al.
Publicado: (2012)

sgBE: a structure-guided design of sgRNA architecture specifies base editing window and enables simultaneous conversion of cytosine and adenosine
por: Wang, Yanhong, et al.
Publicado: (2020)

Combining service design and discrete choice experiments for intervention design: An application to weather index insurance
por: Dehmel, Naira, et al.
Publicado: (2021)

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
por: Omasits, Ulrich, et al.
Publicado: (2013)

Probing the effect of promoters on noise in gene expression using thousands of designed sequences
por: Sharon, Eilon, et al.
Publicado: (2014)

Beta-diversity distance matrices for microbiome sample size and power calculations — How to obtain good estimates
Publicado: (2022)

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
por: Keough, Kathleen C., et al.
Publicado: (2019)

Improved methods for creating migratable Holliday junction substrates
por: Chen, Stefanie Hartman, et al.
Publicado: (2013)

Statistical tools for synthesizing lists of differentially expressed features in related experiments
por: Blangiardo, Marta, et al.
Publicado: (2007)

Cannot write session to /tmp/vufind_sessions/sess_buqvh4gueqg40r5mdcb101evdq