Orchestrating high-throughput genomic analysis with Bioconductor

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis

(2014) Nina Cabezas-Wallscheid et al.   Cell Stem Cell

Comparative Meta-analysis of Prognostic Gene Signatures for Late-Stage Ovarian Cancer

(2014) Levi Waldron et al.   JNCI-Journal of the National Cancer Institute

Risk Prediction for Late-Stage Ovarian Cancer by Meta-analysis of 1525 Patient Samples

(2014) Markus Riester et al.   JNCI-Journal of the National Cancer Institute

Epiviz: interactive visual analytics for functional genomics data

(2014) Florin Chelaru et al.   NATURE METHODS

Scalable Genomics with R and Bioconductor

(2014) Michael Lawrence et al.   STATISTICAL SCIENCE

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

(2014) Greg Finak et al.   PLoS Computational Biology

The anatomy of successful computational biology software

(2013) Stephen Altschul et al.   NATURE BIOTECHNOLOGY

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping

(2013) Christina Laufer et al.   NATURE METHODS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS