TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Authors
Keywords
RNA sequencing, NGS data processing, Data evaluation, Bioinformatics workflow, Galaxy, TRAPLINE, Stem cells
Journal
BMC BIOINFORMATICS
Volume 17, Issue 1, Pages -
Publisher
Springer Nature
Online
2016-01-06
DOI
10.1186/s12859-015-0873-9
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Generation of Murine Cardiac Pacemaker Cell Aggregates Based on ES-Cell-Programming in Combination with Myh6-Promoter-Selection
- (2015) Christian Rimmbach et al. Jove-Journal of Visualized Experiments
- Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
- (2014) Vipin T. Sreedharan et al. BIOINFORMATICS
- MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
- (2014) Krishna R Kalari et al. BMC BIOINFORMATICS
- The BioGRID interaction database: 2015 update
- (2014) Andrew Chatr-aryamontri et al. NUCLEIC ACIDS RESEARCH
- Programming and Isolation of Highly Pure Physiologically and Pharmacologically Functional Sinus-Nodal Bodies from Pluripotent Stem Cells
- (2014) Julia Jeannine Jung et al. Stem Cell Reports
- A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads
- (2014) Stanley Kimbung Mbandi et al. Frontiers in Genetics
- Grape RNA-Seq analysis pipeline environment
- (2013) D. G. Knowles et al. BIOINFORMATICS
- A comparison of methods for differential expression analysis of RNA-seq data
- (2013) Charlotte Soneson et al. BMC BIOINFORMATICS
- Comparison of software packages for detecting differential expression in RNA-seq studies
- (2013) F. Seyednasrollah et al. BRIEFINGS IN BIOINFORMATICS
- Mutations in the NOTCH pathway regulator MIB1 cause left ventricular noncompaction cardiomyopathy
- (2013) Guillermo Luxán et al. NATURE MEDICINE
- An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
- (2013) Cristian Del Fabbro 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
- A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data
- (2012) Vanessa M. Kvam et al. AMERICAN JOURNAL OF BOTANY
- Utilizing RNA-Seq data for de novo coexpression network inference
- (2012) Ovidiu D. Iancu et al. BIOINFORMATICS
- RSeQC: quality control of RNA-seq experiments
- (2012) Liguo Wang et al. BIOINFORMATICS
- Differential analysis of gene regulation at transcript resolution with RNA-seq
- (2012) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
- (2012) Intawat Nookaew 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
- FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads
- (2012) Haibin Xu et al. PLoS One
- 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
- Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
- (2011) Jun Li et al. STATISTICAL METHODS IN MEDICAL RESEARCH
- Improving RNA-Seq expression estimates by correcting for fragment bias
- (2011) Adam Roberts et al. GENOME BIOLOGY
- A probabilistic framework for aligning paired-end RNA-seq data
- (2010) Yin Hu et al. BIOINFORMATICS
- A statistical method for the detection of variants from next-generation resequencing of DNA pools
- (2010) V. Bansal BIOINFORMATICS
- Manipulation of FASTQ data with Galaxy
- (2010) D. Blankenberg et al. BIOINFORMATICS
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
- Functional coupling of α2-isoform Na+/K+-ATPase and Ca2+ extrusion through the Na+/Ca2+-exchanger in cardiomyocytes
- (2010) Fredrik Swift et al. CELL CALCIUM
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Defining transcribed regions using RNA-seq
- (2010) Brian T Wilhelm et al. Nature Protocols
- A scaling normalization method for differential expression analysis of RNA-seq data
- (2010) Mark D Robinson 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
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- Applications of New Sequencing Technologies for Transcriptome Analysis
- (2009) Olena Morozova et al. Annual Review of Genomics and Human Genetics
- ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
- (2009) Gabriela Bindea et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Transcript length bias in RNA-seq data confounds systems biology
- (2009) Alicia Oshlack et al. Biology Direct
- RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing
- (2009) Brian T. Wilhelm et al. METHODS
- Genome sequencing: the third generation
- (2009) Erika Check Hayden NATURE
- Predicting microRNA targets and functions: traps for the unwary
- (2009) William Ritchie et al. NATURE METHODS
- Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
- (2009) Iwanka Kozarewa et al. NATURE METHODS
- Computation for ChIP-seq and RNA-seq studies
- (2009) Shirley Pepke et al. NATURE METHODS
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
- (2009) Daniel Ramsköld et al. PLoS Computational Biology
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
- (2008) J. C. Marioni et al. GENOME RESEARCH
- 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
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now