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

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

Novel microRNAs in silkworm (Bombyx mori)

(2010) Yimei Cai et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

(2010) Peng Cui et al.   GENOMICS

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

rQuant.web: a tool for RNA-Seq-based transcript quantitation

(2010) R. Bohnert et al.   NUCLEIC ACIDS RESEARCH

MAGIA, a web-based tool for miRNA and Genes Integrated Analysis

(2010) G. Sales et al.   NUCLEIC ACIDS RESEARCH

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Doron Betel et al.   GENOME BIOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments

(2009) Michael Hackenberg et al.   NUCLEIC ACIDS RESEARCH

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY