RseqFlow: workflows for RNA-Seq data analysis

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

(2010) Sudeep Srivastava et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

(2009) Yangho Chen et al.   BIOINFORMATICS

inGAP: an integrated next-generation genome analysis pipeline

(2009) Ji Qi et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Scaling up workflow-based applications

(2009) Scott Callaghan et al.   JOURNAL OF COMPUTER AND SYSTEM SCIENCES

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