A comprehensive simulation study on classification of RNA-Seq data

MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development

(2015) Selcuk Korkmaz et al.   PLoS One

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform

(2014) Ram Shrestha et al.   BMC BIOINFORMATICS

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Differential Diagnosis of Renal Tumors With Clear Cytoplasm: Clinical Relevance of Renal Tumor Subclassification in the Era of Targeted Therapies and Personalized Medicine

(2013) Rajen Goyal et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

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

(2013) Y. Liao et al.   BIOINFORMATICS

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

(2013) Danni Yu et al.   BIOINFORMATICS

A blood based 12-miRNA signature of Alzheimer disease patients

(2013) Petra Leidinger et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Classification and clustering of sequencing data using a Poisson model

(2011) Daniela M. Witten   Annals of Applied Statistics

A powerful and flexible approach to the analysis of RNA sequence count data

(2011) Yi-Hui Zhou et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

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

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

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

(2009) Joshua S Bloom et al.   BMC GENOMICS

Multiclass cancer classification by support vector machines with class-wise optimized genes and probability estimates

(2009) Ashish Anand et al.   JOURNAL OF THEORETICAL BIOLOGY

A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

(2008) Alexander Statnikov et al.   BMC BIOINFORMATICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

An integrated algorithm for gene selection and classification applied to microarray data of ovarian cancer

(2007) Zne-Jung Lee   ARTIFICIAL INTELLIGENCE IN MEDICINE