Publications by authors named "Herve Pages"

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Orchestrating Spatial Transcriptomics Analysis with Bioconductor.
Helena L Crowell, Yixing Dong, Ilaria Billato, Peiying Cai, Martin Emons

bioRxiv· November 2025

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Benchmarking large-scale single-cell RNA-seq analysis.
Ilaria Billato, Herve Pages, Vince Carey, Levi Waldron, Gabriele Sales

bioRxiv· October 2025

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Bioconductor's Computational Ecosystem for Genomic Data Science in Cancer.
Marcel Ramos, Lori Shepherd, Nathan C Sheffield, Alexandru Mahmoud, Hervé Pagès

Methods Mol Biol· August 2025

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Eleven quick tips for writing a Bioconductor package.
Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer

PLoS Comput Biol· March 2025

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restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor.
Shweta Gopaulakrishnan, Samuela Pollack, B J Stubbs, Hervé Pagès, John Readey

F1000Res· June 2020

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Orchestrating single-cell analysis with Bioconductor.
Robert A Amezquita, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp

Nat Methods· February 2020

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Publisher Correction: Orchestrating single-cell analysis with Bioconductor.
Robert A Amezquita, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp

Nat Methods· February 2020

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Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin.
Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan, Hervé Pagès

Genome Res· August 2019

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beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.
Aaron T L Lun, Hervé Pagès, Mike L Smith

PLoS Comput Biol· May 2018

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GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.
Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès, Alper Kucukural

BMC Genomics· May 2017

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Genomic Annotation Resources in R/Bioconductor.
Marc R J Carlson, Hervé Pagès, Sonali Arora, Valerie Obenchain, Martin Morgan

Methods Mol Biol· December 2016

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Orchestrating high-throughput genomic analysis with Bioconductor.
Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson

Nat Methods· February 2015

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Software for computing and annotating genomic ranges.
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson

PLoS Comput Biol· February 2014

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ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.
Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin

BMC Bioinformatics· May 2010

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ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Hervé Pagès

Bioinformatics· October 2009

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