V. Carey

发表

Bioconductor: open software development for computational biology and bioinformatics

Jean YH Yang, K. Hornik, L. Tierney, 2004, Genome Biology.

Mixed-Effects Models in S and S-Plus

V. Carey, You-Gan Wang, Vincent J. Carey, 2001 .

Unsupervised Machine Learning

Robert Gentleman, V. J. Carey, R. Gentleman, 2008 .

Graphs in molecular biology

Robert Gentleman, Li Long, Wolfgang Huber, 2007, BMC Bioinformatics.

Working correlation structure misspecification, estimation and covariate design: Implications for generalised estimating equations performance

V. Carey, You‐Gan Wang, 2003 .

Criteria for Working–Correlation–Structure Selection in GEE

V. Carey, You‐Gan Wang, L. Hin, 2007 .

Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole genome sequencing studies at scale

Ivana V. Yang, Andrew D. Johnson, Ryan D. Hernandez, 2020, Nature Genetics.

Graphical Models: Methods for Data Analysis and Mining

V. Carey, 2003 .

Bayesian Inference on Protective Antibody Levels Using Case‐Control Data

V. Carey, C. Baker, R. Platt, 2001, Biometrics.

Buffet-Style Expression Factor-Adjusted Discovery Increases the Yield of Robust Expression Quantitative Trait Loci

M. Obeidat, P. Paré, E. Silverman, 2015, bioRxiv.

The interaction between equipoise and logistics in clinical trials: A case study

V. Carey, H. Spiegel, E. Abrams, 2017, Clinical trials.

Introduction and Motivating Examples

Robert Gentleman, W. Huber, Vincent J. Carey, 2005 .

Software for Computing and Annotating Genomic Ranges The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters

Martin T. Morgan, R. Gentleman, W. Huber, 2013 .

GEE solvers: case studies in DSC design and implementation

V. Carey, 2001 .

TFutils: Data structures for transcription factor bioinformatics

N. Pochet, V. Carey, K. Glass, 2019, F1000Research.

TFutils: Data structures for transcription factor bioinformatics.

N. Pochet, V. Carey, K. Glass, 2019, F1000Research.

GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Daniel J. Blankenberg, Jaclyn N. Taroni, Marcel Ramos, 2020, bioRxiv.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Brian D. O’Connor, Ira M. Hall, Martin T. Morgan, 2022, Cell genomics.

Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

Andrew D. Johnson, May E. Montasser, Nicholette D. Palmer, 2022, Nature Genetics.

Bioinformatics and Computational Biology Solutions using R and Bioconductor

Rafael A. Irizarry, Sandrine Dudoit, Robert Gentleman, 2005 .

GGtools: analysis of genetics of gene expression in bioconductor

Robert Gentleman, Ross Lazarus, Vincent J. Carey, 2007, Bioinform..

Bioconductor: an open source framework for bioinformatics and computational biology.

Vincent J Carey, Mark Reimers, V. Carey, 2006, Methods in enzymology.

Orchestrating single-cell analysis with Bioconductor

Raphael Gottardo, Charlotte Soneson, Stephanie C. Hicks, 2019, Nature Methods.

Orchestrating high-throughput genomic analysis with Bioconductor

Raphael Gottardo, Robert Gentleman, Wolfgang Huber, 2015, Nature Methods.

Software for Computing and Annotating Genomic Ranges

Robert Gentleman, Wolfgang Huber, Hervé Pagès, 2013, PLoS Comput. Biol..

rtracklayer: an R package for interfacing with genome browsers

Robert Gentleman, Michael F. Lawrence, Vincent J. Carey, 2009, Bioinform..

Community-wide hackathons to identify central themes in single-cell multi-omics

Matthew E. Ritchie, Joshua D. Welch, Lauren L. Hsu, 2021, Genome Biology.

deconvSeq: deconvolution of cell mixture distribution in sequencing data

Rose Du, Vince Carey, Scott Weiss, 2019, Bioinform..

Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes

B. Haas, J. Mesirov, N. Pochet, 2020, JCO clinical cancer informatics.

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

Paul Shannon, Michael F. Lawrence, Vincent J. Carey, 2014, Bioinform..

Machine Learning and Its Applications to Biology

Sorin Draghici, Adi L. Tarca, Roberto Romero, 2007, PLoS Comput. Biol..

Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor

Martin T. Morgan, Marcel Ramos, L. Waldron, 2021 .

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

Brian D. O’Connor, Ira M. Hall, Martin T. Morgan, 2021, bioRxiv.

GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Daniel J. Blankenberg, Jaclyn N. Taroni, Marcel Ramos, 2022, Nature Communications.

Network structures and algorithms in Bioconductor

Robert Gentleman, Vincent J. Carey, Jeff Gentry, 2005, Bioinform..

The Bioconductor channel in F1000Research

Martin T. Morgan, K. Hansen, V. Carey, 2016, F1000Research.

An Algorithm for Clustered Data Generalized Additive Modelling with S-PLUS

V. Carey, L. Hin, 2005 .

Toward a gold standard for benchmarking gene set enrichment analysis

Ralf Zimmer, Levi Waldron, Charity W. Law, 2019, bioRxiv.

Public data and open source tools for multi-assay genomic investigation of disease

Aedín C. Culhane, David Gomez-Cabrero, Zhaleh Safikhani, 2015, Briefings Bioinform..

Multiomic Integration of Public Oncology Databases in Bioconductor

Martin T. Morgan, Lucas Schiffer, Marcel Ramos, 2020, JCO clinical cancer informatics.

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x

Robert Gentleman, Michael F. Lawrence, Vincent J. Carey, 2009, Bioinform..

Working covariance model selection for generalized estimating equations

You-Gan Wang, V. Carey, You‐Gan Wang, 2011, Statistics in medicine.

Software for the integration of multi-omics experiments in Bioconductor

Benjamin Haibe-Kains, David Gomez-Cabrero, Angela Re, 2017, bioRxiv.

Unbiased Estimating Equations From Working Correlation Models for Irregularly Timed Repeated Measures

Vincent J. Carey, You-Gan Wang, V. Carey, 2004 .

An extensible application for assembling annotation for genomic data

Robert Gentleman, Jianhua Zhang, Vincent J. Carey, 2003, Bioinform..

Visualization and Annotation of Genomic Experiments

Vincent J. Carey, Robert Gentleman, R. Gentleman, 2003 .

Supervised Machine Learning

R. Gentleman, W. Huber, V. Carey, 2020, Methodology of Educational Measurement and Assessment.

Clinical trial data access: Opening doors with TrialShare.

V. Carey, D. Rotrosen, A. Asare, 2016, The Journal of allergy and clinical immunology.

Method Bioconductor: open software development for computational biology and bioinformatics

K. Hornik, R. Gentleman, F. Leisch, 2004 .

Bioconductor: an open source framework for bioinformatics and computational biology.

V. Carey, M. Reimers, 2006, Methods in enzymology.

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

Michael F. Lawrence, Martin T. Morgan, P. Shannon, 2014, Bioinform..

GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Daniel J. Blankenberg, Jaclyn N. Taroni, Marcel Ramos, 2021, bioRxiv.

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem

Matthew E. Ritchie, Martin T. Morgan, V. Carey, 2019, bioRxiv.

Toward a gold standard for benchmarking gene set enrichment analysis

Ralf Zimmer, Levi Waldron, Sean Davis, 2020, Briefings Bioinform..

Bioconductor Project Bioconductor Project Working Papers Year Paper Bioconductor : Open software development for computational biology and bioinformatics

K. Hornik, R. Gentleman, F. Leisch, 2013 .