miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis

Omics Pipe: a community-based framework for reproducible multi-omics data analysis

(2015) Kathleen M. Fisch et al.   BIOINFORMATICS

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

(2015) Mattia D'Antonio et al.   BMC GENOMICS

sRNAtoolbox: an integrated collection of small RNA research tools

(2015) Antonio Rueda et al.   NUCLEIC ACIDS RESEARCH

miRGate: a curated database of human, mouse and rat miRNA–mRNA targets

(2015) Eduardo Andrés-León et al.   Database-The Journal of Biological Databases and Curation

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

(2015) Yuan Gao et al.   GENOME BIOLOGY

BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data

(2014) H. Chae et al.   BIOINFORMATICS

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

(2014) Krishna R Kalari et al.   BMC BIOINFORMATICS

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

(2014) Tiezheng Yuan et al.   BMC GENOMICS

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

(2014) Zhifu Sun et al.   BMC GENOMICS

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia

(2014) Carme Camps et al.   Molecular Cancer

RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells

(2014) Blanca E. Himes et al.   PLoS One

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

(2014) Nuno A. Fonseca et al.   PLoS One

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Grape RNA-Seq analysis pipeline environment

(2013) D. G. Knowles et al.   BIOINFORMATICS

iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq

(2013) Giorgio Giurato et al.   BMC BIOINFORMATICS

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

TCW: Transcriptome Computational Workbench

(2013) Carol Soderlund et al.   PLoS One

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

(2013) Jinyu Wu et al.   RNA Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation

(2012) V. Williamson et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

wapRNA: a web-based application for the processing of RNA sequences

(2011) Wenming Zhao et al.   BIOINFORMATICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

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

(2011) M. Hackenberg et al.   NUCLEIC ACIDS RESEARCH

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer 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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

DSAP: deep-sequencing small RNA analysis pipeline

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

(2009) Wei-Chi Wang et al.   BMC BIOINFORMATICS

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

A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions

(2008) C. J. Creighton et al.   RNA