eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing

Characterization of human plasma-derived exosomal RNAs by deep sequencing

(2013) Xiaoyi Huang et al.   BMC GENOMICS

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

miRspring: a compact standalone research tool for analyzing miRNA-seq data

(2013) David T. Humphreys et al.   NUCLEIC ACIDS RESEARCH

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

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

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

(2012) Yue Li 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

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

New methods for next generation sequencing based microRNA expression profiling

(2011) Henk PJ Buermans et al.   BMC GENOMICS

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

(2011) M. Hackenberg et al.   NUCLEIC ACIDS 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

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

(2011) Brad A Friedman et al.   GENOME BIOLOGY

miRNAkey: a software for microRNA deep sequencing analysis

(2010) Roy Ronen et al.   BIOINFORMATICS

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

(2010) Anthony Mathelier et al.   BIOINFORMATICS

DSAP: deep-sequencing small RNA analysis pipeline

(2010) Po-Jung Huang et al.   NUCLEIC ACIDS RESEARCH

mirTools: microRNA profiling and discovery based on high-throughput sequencing

(2010) Erle Zhu et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY