Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective
Authors
Keywords
-
Journal
BRIEFINGS IN BIOINFORMATICS
Volume 17, Issue 2, Pages 213-223
Publisher
Oxford University Press (OUP)
Online
2015-06-25
DOI
10.1093/bib/bbv036
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- RNASeqGUI: a GUI for analysing RNA-Seq data
- (2014) Francesco Russo et al. BIOINFORMATICS
- PRADA: pipeline for RNA sequencing data analysis
- (2014) Wandaliz Torres-García et al. BIOINFORMATICS
- piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing
- (2014) Bo W. Han et al. BIOINFORMATICS
- SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data
- (2014) Yan Peng et al. BMC BIOINFORMATICS
- SMITH: a LIMS for handling next-generation sequencing workflows
- (2014) Francesco Venco et al. BMC BIOINFORMATICS
- MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
- (2014) Krishna R Kalari et al. BMC BIOINFORMATICS
- Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress
- (2014) Kyuri Jo et al. METHODS
- RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
- (2014) Guorong Xu et al. PLoS One
- Grape RNA-Seq analysis pipeline environment
- (2013) D. G. Knowles et al. BIOINFORMATICS
- NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets
- (2013) Marcus R. Breese et al. BIOINFORMATICS
- Finishing bacterial genome assemblies with Mix
- (2013) Hayssam Soueidan et al. BMC BIOINFORMATICS
- Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
- (2013) Simon Anders et al. Nature Protocols
- TCW: Transcriptome Computational Workbench
- (2013) Carol Soderlund et al. PLoS One
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
- (2013) Daehwan Kim et al. GENOME BIOLOGY
- Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
- (2013) Franck Rapaport et al. GENOME BIOLOGY
- Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells
- (2013) Amar M. Singh et al. Stem Cell Reports
- FX: an RNA-Seq analysis tool on the cloud
- (2012) Dongwan Hong et al. BIOINFORMATICS
- easyRNASeq: a bioconductor package for processing RNA-Seq data
- (2012) N. Delhomme et al. BIOINFORMATICS
- RNA-SeQC: RNA-seq metrics for quality control and process optimization
- (2012) David S. DeLuca et al. BIOINFORMATICS
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data
- (2012) Vinay K. Mittal et al. NUCLEIC ACIDS RESEARCH
- RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
- (2012) M. Lohse et al. NUCLEIC ACIDS RESEARCH
- RseqFlow: workflows for RNA-Seq data analysis
- (2011) Ying Wang et al. BIOINFORMATICS
- wapRNA: a web-based application for the processing of RNA sequences
- (2011) Wenming Zhao et al. BIOINFORMATICS
- A pipeline for RNA-seq data processing and quality assessment
- (2011) Angela Goncalves et al. BIOINFORMATICS
- RNA-Seq analysis in MeV
- (2011) E. A. Howe et al. BIOINFORMATICS
- Chipster: user-friendly analysis software for microarray and other high-throughput data
- (2011) M Aleksi Kallio et al. BMC GENOMICS
- Differential expression in RNA-seq: A matter of depth
- (2011) S. Tarazona et al. GENOME RESEARCH
- GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
- (2011) Jason S. Cumbie et al. PLoS One
- S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
- (2011) Matthias Zytnicki et al. PLoS One
- ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
- (2011) Brad A Friedman et al. GENOME BIOLOGY
- Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
- (2011) Ernest Turro et al. GENOME BIOLOGY
- RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
- (2010) Lukas Habegger et al. BIOINFORMATICS
- baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
- (2010) Thomas J Hardcastle et al. BMC BIOINFORMATICS
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- Understanding the pathogenesis of Alzheimer’s disease: will RNA-Seq realize the promise of transcriptomics?
- (2010) Greg T. Sutherland et al. JOURNAL OF NEUROCHEMISTRY
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- The Sequence Read Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- Cloud-scale RNA-sequencing differential expression analysis with Myrna
- (2010) Ben Langmead et al. GENOME BIOLOGY
- Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
- (2010) Jeremy Goecks et al. GENOME BIOLOGY
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
- (2009) L. W. Hillier et al. GENOME RESEARCH
- Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
- (2009) Steffen Durinck et al. Nature Protocols
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
Become a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get StartedAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started