Search Results - Leonardo Collado-Torres

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  1. 1
    recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]

    recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations] by Leonardo Collado-Torres, Abhinav Nellore, Andrew E. Jaffe

    Published 2017-08-01
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  2. 2
    regionReport: Interactive reports for region-level and feature-level genomic analyses [version 2; referees: 2 approved, 1 approved with reservations]

    regionReport: Interactive reports for region-level and feature-level genomic analyses [version 2; referees: 2 approved, 1 approved with reservations] by Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek

    Published 2016-06-01
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  3. 3
    BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data

    BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data by Nicholas J. Eagles, Richard Wilton, Andrew E. Jaffe, Leonardo Collado-Torres

    Published 2023-09-01
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  4. 4
    Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses

    Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses by Helena Kuri-Magaña, Helena Kuri-Magaña, Leonardo Collado-Torres, Leonardo Collado-Torres, Andrew E. Jaffe, Andrew E. Jaffe, Andrew E. Jaffe, Andrew E. Jaffe, Humberto Valdovinos-Torres, Marbella Ovilla-Muñoz, Juan Téllez-Sosa, Laura C. Bonifaz, Jesús Martínez-Barnetche

    Published 2018-11-01
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  5. 5
    SynGAP isoforms differentially regulate synaptic plasticity and dendritic development

    SynGAP isoforms differentially regulate synaptic plasticity and dendritic development by Yoichi Araki, Ingie Hong, Timothy R Gamache, Shaowen Ju, Leonardo Collado-Torres, Joo Heon Shin, Richard L Huganir

    Published 2020-06-01
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  6. 6
    Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

    Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments by Chaichontat Sriworarat, Annie Nguyen, Nicholas J. Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R. Maynard, Stephanie C. Hicks

    Published 2023-01-01
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  7. 7
    Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets

    Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets by Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks, Kristen R. Maynard

    Published 2023-12-01
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  8. 8
    Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue

    Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue by Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Stephanie C. Page, Stephanie C. Hicks, Kristen R. Maynard, Leonardo Collado-Torres

    Published 2023-10-01
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  9. 9
    spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

    spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data by Brenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Page, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard, Leonardo Collado-Torres

    Published 2022-06-01
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  10. 10
    Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

    Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods by Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger, Joo Heon Shin

    Published 2019-06-01
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  11. 11
    Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

    Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex by Kira A. Perzel Mandell, Amanda J. Price, Richard Wilton, Leonardo Collado-Torres, Ran Tao, Nicholas J. Eagles, Alexander S. Szalay, Thomas M. Hyde, Daniel R. Weinberger, Joel E. Kleinman, Andrew E. Jaffe

    Published 2021-01-01
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  12. 12
    Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses

    Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses by Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres

    Published 2021-07-01
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  13. 13
    Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation

    Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation by Amanda J. Price, Leonardo Collado-Torres, Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe

    Published 2019-09-01
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  14. 14
    SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

    SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses by Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres

    Published 2021-05-01
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  15. 15
    recount3: summaries and queries for large-scale RNA-seq expression and splicing

    recount3: summaries and queries for large-scale RNA-seq expression and splicing by Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D. Hansen, Ben Langmead

    Published 2021-11-01
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  16. 16
    Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk

    Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk by Kira A. Perzel Mandell, Nicholas J. Eagles, Richard Wilton, Amanda J. Price, Stephen A. Semick, Leonardo Collado-Torres, William S. Ulrich, Ran Tao, Shizhong Han, Alexander S. Szalay, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe

    Published 2021-09-01
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  17. 17
    VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data

    VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data by Madhavi Tippani, Heena R. Divecha, Joseph L. Catallini, Sang H. Kwon, Lukas M. Weber, Abby Spangler, Andrew E. Jaffe, Thomas M. Hyde, Joel E. Kleinman, Stephanie C. Hicks, Keri Martinowich, Leonardo Collado-Torres, Stephanie C. Page, Kristen R. Maynard

    Published 2023-01-01
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  18. 18
    The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics by Lukas M Weber, Heena R Divecha, Matthew N Tran, Sang Ho Kwon, Abby Spangler, Kelsey D Montgomery, Madhavi Tippani, Rahul Bharadwaj, Joel E Kleinman, Stephanie C Page, Thomas M Hyde, Leonardo Collado-Torres, Kristen R Maynard, Keri Martinowich, Stephanie C Hicks

    Published 2024-01-01
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  19. 19
    Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus

    Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus by Kynon J. M. Benjamin, Ria Arora, Arthur S. Feltrin, Geo Pertea, Hunter H. Giles, Joshua M. Stolz, Laura D’Ignazio, Leonardo Collado-Torres, Joo Heon Shin, William S. Ulrich, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Apuã C. M. Paquola, Jennifer A. Erwin

    Published 2024-05-01
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  20. 20
    TrkB-dependent regulation of molecular signaling across septal cell types

    TrkB-dependent regulation of molecular signaling across septal cell types by Lionel A. Rodriguez, Matthew Nguyen Tran, Renee Garcia-Flores, Seyun Oh, Robert A. Phillips, Elizabeth A. Pattie, Heena R. Divecha, Sun Hong Kim, Joo Heon Shin, Yong Kyu Lee, Carly Montoya, Andrew E. Jaffe, Leonardo Collado-Torres, Stephanie C. Page, Keri Martinowich

    Published 2024-01-01
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