Bioinformatics – Next Gen Sequencing – Virtual Issue

Bioinformatics has published a Next-Gen Sequencing “Virtual Issue” covering all the sequencing tools that appeared in the journal.  We have listed those described as applicable to RNA-Seq.

Statistical Inferences for Isoform Expression in RNA-Seq.
Hui Jiang and Wing Wong
Bioinformatics (2009) 25: 1026–1032 Full Text

A toolkit for analysing large-scale plant small RNA datasets
Simon Moxon et al.
Bioinformatics (2008) 24: 2252-2253 Full Text

TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell et al.
Bioinformatics (2009) 25: 1105–1111 Full Text

RNA-MATE: A recursive mapping strategy for high-throughput RNA-sequencing data
Nicole Cloonan et al.
Bioinformatics (2009) 25: 2615-6 Full Text

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Likun Wang et al.
Bioinformatics (2010) 26: 136-138 Full Text

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Jacob Degner et al.
Bioinformatics (2009) 25: 3207-3212 Full Text

Supersplat–spliced RNA-seq alignment
Douglas Bryant Jnr. et al.
Bioinformatics (2010) 26: 1500–1505 Full Text

RNA-Seq gene expression estimation with read mapping uncertainty
Bo Li et al.
Bioinformatics (2010) 26: 518-528 Full Text

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark Robinson et al.
Bioinformatics (2010) 26: 139–140 Full Text

Length Bias Correction for RNA-seq Data in Gene Set Analyses
Liyan Gao et al
Bioinformatics (2011) 27: 662–669 Full Text

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq
Zhengpeng Wu et al
Bioinformatics (2011) 27: 502-508 Full Text

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
Lukas Habegger et al
Bioinformatics (2011) 27: 281-283 Full Text

htSeqTools: High-Throughput Sequencing Quality Control, Processing and Visualization in R
Evarist Planet et al
Advanced Access publication: 22 December 2011 Full text

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq
Ming Hu et al
Bioinformatics (2012) 28: 63-68 Full Text

deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns
David Langenberger et al
Bioinformatics (2012) 28: 17-24 Full Text

RNA-Seq Analysis in MeV
Eleanor Howe et al
Bioinformatics (2011) 27: 3209-3210 Full Text