RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

(2011) Tzi-Yuan Wang et al.   Biotechnology for Biofuels

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

(2011) Prabin Bajgain et al.   BMC GENOMICS

De Novo Assembly of Expressed Transcripts and Global Analysis of the Phalaenopsis aphrodite Transcriptome

(2011) Chun-lin Su et al.   PLANT AND CELL PHYSIOLOGY

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

(2011) Stefan Siebert et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis

(2010) M. Lohse et al.   PLANT PHYSIOLOGY

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

(2009) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

BioJava: an open-source framework for bioinformatics

(2008) R. C. G. Holland et al.   BIOINFORMATICS