Bilaketaren emaitzak - Davis J. McCarthy

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  1. 1
    Testing significance relative to a fold-change threshold is a TREAT

    Testing significance relative to a fold-change threshold is a TREAT nork Davis J. McCarthy, Gordon K. Smyth

    Argitaratua 2009
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  2. 2
    A comparison of marker gene selection methods for single-cell RNA sequencing data

    A comparison of marker gene selection methods for single-cell RNA sequencing data nork Jeffrey M. Pullin, Davis J. McCarthy

    Argitaratua 2024
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  3. 3
    Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

    Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference nork Yuanhua Huang, Davis J. McCarthy, Oliver Stegle

    Argitaratua 2019
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  4. 4
    Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

    Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation nork Davis J. McCarthy, Yunshun Chen, Gordon K. Smyth

    Argitaratua 2012
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  5. 5
    <tt>edgeR</tt>: a Bioconductor package for differential expression analysis of digital gene expression data

    <tt>edgeR</tt>: a Bioconductor package for differential expression analysis of digital gene expression data nork Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth

    Argitaratua 2009
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  6. 6
    A step-by-step workflow for low-level analysis of single-cell RNA-seq data

    A step-by-step workflow for low-level analysis of single-cell RNA-seq data nork Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni

    Argitaratua 2016
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  7. 7
    A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

    A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor nork Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni

    Argitaratua 2016
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  8. 8
    Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates

    Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates nork Steven P. Lund, Dan Nettleton, Davis J. McCarthy, Gordon K. Smyth

    Argitaratua 2012
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  9. 9
    Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

    Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R nork Davis J. McCarthy, Kieran R. Campbell, Aaron T. L. Lun, Quin F. Wills

    Argitaratua 2016
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  10. 10
    f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq

    f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq nork Florian Buettner, Ploy N. Pratanwanich, Davis J. McCarthy, John C. Marioni, Oliver Stegle

    Argitaratua 2017
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  11. 11
    Optimizing expression quantitative trait locus mapping workflows for single-cell studies

    Optimizing expression quantitative trait locus mapping workflows for single-cell studies nork Anna Cuomo, Giordano Alvari, Christina B. Azodi, Davis J. McCarthy, Marc Jan Bonder

    Argitaratua 2021
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  12. 12
    SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset

    SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset nork Ruqian Lyu, Annika Vannan, Jonathan A. Kropski, Nicholas E. Banovich, Davis J. McCarthy

    Argitaratua 2025
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  13. 13
    Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

    Count-based differential expression analysis of RNA sequencing data using R and Bioconductor nork Simon Anders, Davis J. McCarthy, Yunshun Chen, Michał Okoniewski, Gordon K. Smyth, Wolfgang Huber, Mark D. Robinson

    Argitaratua 2013
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  14. 14
    Choice of transcripts and software has a large effect on variant annotation

    Choice of transcripts and software has a large effect on variant annotation nork Davis J. McCarthy, Peter Humburg, Alexander Kanapin, Manuel A. Rivas, Kyle J. Gaulton, Jean‐Baptiste Cazier, Peter Donnelly

    Argitaratua 2014
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  15. 15
    Classification of low quality cells from single-cell RNA-seq data

    Classification of low quality cells from single-cell RNA-seq data nork Tomislav Ilicic, Jong Kim, Aleksandra A. Kolodziejczyk, Frederik Otzen Bagger, Davis J. McCarthy, John C. Marioni, Sarah A. Teichmann

    Argitaratua 2016
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  16. 16
    Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

    Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity nork Stephanie M. Linker, Lara Urban, Stephen J. Clark, Mariya Chhatriwala, Shradha Amatya, Davis J. McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle, Marc Jan Bonder

    Argitaratua 2019
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  17. 17
    Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

    Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods nork Drew Neavin, Anne Senabouth, Himanshi Arora, Jimmy Tsz Hang Lee, Aida Ripoll-Cladellas, Lude Franke, Shyam Prabhakar, Chun Ye, Davis J. McCarthy, Marta Melé, Martin Hemberg, Joseph E. Powell

    Argitaratua 2024
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  18. 18
    Visualization of Biomedical Data

    Visualization of Biomedical Data nork Séan O’Donoghue, Benedetta F. Baldi, Susan J. Clark, Aaron E. Darling, James M. Hogan, Sandeep Kaur, Lena Maier‐Hein, Davis J. McCarthy, William J. Moore, Esther Stenau, Jason R. Swedlow, Jenny Vuong, James B Procter

    Argitaratua 2018
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  19. 19
    Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics

    Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics nork Loukia Yiangou, Rodrigo A. Grandy, Carola Maria Morell, Rute A. Tomaz, Anna Osnato, Juned Kadiwala, Daniele Muraro, José Garcia‐Bernardo, Shota Nakanoh, William G. Bernard, Daniel Ortmann, Davis J. McCarthy, Ingrid Simonic, Sanjay Sinha, Ludovic Vallier

    Argitaratua 2018
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  20. 20
    Cell type-specific and disease-associated eQTL in the human lung

    Cell type-specific and disease-associated eQTL in the human lung nork Heini M. Natri, Christina B. Azodi, Lance Peter, Chase J. Taylor, Sagrika Chugh, Robert Kendle, Mei-I Chung, David K. Flaherty, Brittany K. Matlock, Carla L. Calvi, Timothy S. Blackwell, Lorraine B. Ware, Matthew Bacchetta, Rajat Walia, Ciara M. Shaver, Jonathan A. Kropski, Davis J. McCarthy, Nicholas E. Banovich

    Argitaratua 2023
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