Cargando…

Getting the most out of RNA-seq data analysis

Background. A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally, or use them for downstream systems biology analysis. Producing a coherent differentia...

Descripción completa

Detalles Bibliográficos
Autores principales:	Khang, Tsung Fei, Lau, Ching Yee
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2015
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631466/ https://www.ncbi.nlm.nih.gov/pubmed/26539333 http://dx.doi.org/10.7717/peerj.1360

Ejemplares similares

clrDV: a differential variability test for RNA-Seq data based on the skew-normal distribution
por: Li, Hongxiang, et al.
Publicado: (2023)

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
por: Dimitrov, Daniel, et al.
Publicado: (2020)

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
por: Zhu, Xun, et al.
Publicado: (2017)

Power analysis and sample size estimation for RNA-Seq differential expression
por: Ching, Travers, et al.
Publicado: (2014)

Error estimates for the analysis of differential expression from RNA-seq count data
por: Burden, Conrad J., et al.
Publicado: (2014)

SingleCAnalyzer: Interactive Analysis of Single Cell RNA-Seq Data on the Cloud
por: Prieto, Carlos, et al.
Publicado: (2022)

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism
por: McClure, Ryan S., et al.
Publicado: (2023)

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
por: Golosova, Olga, et al.
Publicado: (2014)

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
por: Koçhan, Necla, et al.
Publicado: (2019)

voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data
por: Zararsiz, Gokmen, et al.
Publicado: (2017)

On the classification of simple and complex biological images using Krawtchouk moments and Generalized pseudo-Zernike moments: a case study with fly wing images and breast cancer mammograms
por: Goh, Jia Yin, et al.
Publicado: (2021)

Cross-platform normalization of microarray and RNA-seq data for machine learning applications
por: Thompson, Jeffrey A., et al.
Publicado: (2016)

Identifying stably expressed genes from multiple RNA-Seq data sets
por: Zhuo, Bin, et al.
Publicado: (2016)

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data
por: Coudray, Alexandre, et al.
Publicado: (2018)

Variance component testing for identifying differentially expressed genes in RNA-seq data
por: Yang, Sheng, et al.
Publicado: (2017)

Detection of condition-specific marker genes from RNA-seq data with MGFR
por: El Amrani, Khadija, et al.
Publicado: (2019)

Integrated mRNA-seq and miRNA-seq analysis of goat fibroblasts response to Brucella Melitensis strain M5-90
por: Li, Baobao, et al.
Publicado: (2021)

A robust semi-supervised NMF model for single cell RNA-seq data
por: Wu, Peng, et al.
Publicado: (2020)

First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data
por: Brüwer, Jan D., et al.
Publicado: (2018)

A clustering method for small scRNA-seq data based on subspace and weighted distance
por: Ning, Zilan, et al.
Publicado: (2023)

Cell annotation using scRNA-seq data: A protein-protein interaction network approach
por: Senra, Daniela, et al.
Publicado: (2023)

Biological classification with RNA-seq data: Can alternatively spliced transcript expression enhance machine learning classifiers?
por: Johnson, Nathan T., et al.
Publicado: (2018)

pulseTD: RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data
por: Wang, Xin, et al.
Publicado: (2020)

Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL)
por: Kyritsis, Konstantinos A., et al.
Publicado: (2023)

A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data
por: Srinivasan, Suhas, et al.
Publicado: (2020)

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies
por: Cabau, Cédric, et al.
Publicado: (2017)

Analysis of the in planta transcriptome expressed by the corn pathogen Pantoea stewartii subsp. stewartii via RNA-Seq
por: Packard, Holly, et al.
Publicado: (2017)

kakapo: easy extraction and annotation of genes from raw RNA-seq reads
por: Ramanauskas, Karolis, et al.
Publicado: (2023)

Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort
por: Nirgude, Snehal, et al.
Publicado: (2023)

cdev: a ground-truth based measure to evaluate RNA-seq normalization performance
por: Tran, Diem-Trang, et al.
Publicado: (2021)

Gene representation in scRNA-seq is correlated with common motifs at the 3′ end of transcripts
por: Li, Xinling, et al.
Publicado: (2023)

Validating a re-implementation of an algorithm to integrate transcriptome and ChIP-seq data
por: Ahmed, Mahmoud, et al.
Publicado: (2023)

bestDEG: a web-based application automatically combines various tools to precisely predict differentially expressed genes (DEGs) from RNA-Seq data
por: Sangket, Unitsa, et al.
Publicado: (2022)

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
por: Waardenberg, Ashley J., et al.
Publicado: (2019)

Intracellular and Intercellular Gene Regulatory Network Inference From Time-Course Individual RNA-Seq
por: Kashima, Makoto, et al.
Publicado: (2021)

CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
por: Maragkakis, Manolis, et al.
Publicado: (2016)

Seq2science: an end-to-end workflow for functional genomics analysis
por: van der Sande, Maarten, et al.
Publicado: (2023)

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols
por: Combs, Peter A., et al.
Publicado: (2015)

Reconstruction of insect hormone pathways in an aquatic firefly, Sclerotia aquatilis (Coleoptera: Lampyridae), using RNA-seq
por: Chanchay, Pornchanan, et al.
Publicado: (2019)

RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
por: Ee Uli, Joey, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_ui494feqifk1su3h2f397qe90t