L. Collado-Torres
L. Collado-Torres
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escheR: Unified multi-dimensional visualizations with Gestalt principles
The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are …
Boyi Guo
,
Louise A. Huuki-Myers
,
Melissa Grant-Peters
,
Leonardo Collado-Torres
,
Stephanie C. Hicks
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DOI
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Bioconductor
Influence of Alzheimer’s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex
Neuropathological lesions in the brains of individuals affected with neurodegenerative disorders are hypothesized to trigger molecular …
Sang Ho Kwon
,
Sowmya Parthiban
,
Madhavi Tippani
,
Heena R. Divecha
,
Nicholas J. Eagles
,
Jashandeep S. Lobana
,
Stephen R. Williams
,
Michelle Mak
,
Rahul A. Bharadwaj
,
Joel E. Kleinman
,
Thomas M. Hyde
,
Stephanie C. Page
,
Stephanie C. Hicks †
,
Keri Martinowich †
,
Kristen R. Maynard †
,
Leonardo Collado-Torres †
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Project
DOI
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Code
Documentation
Splicing accuracy varies across human introns, tissues and age
Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and …
S García-Ruiz
,
D Zhang
,
E K Gustavsson, G Rocamora-Perez
,
M Grant-Peters
,
A Fairbrother-Browne
,
R H Reynolds
,
J W Brenton
,
A L Gil-Martínez
,
Z Chen
,
D C Rio
,
J A Botia
,
S Guelfi
,
Leonardo Collado-Torres
,
M Ryten
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Genetic and environmental contributions to ancestry differences in gene expression in the human brain
Ancestral differences in genomic variation are determining factors in gene regulation; however, most gene expression studies have been …
Kynon J.M. Benjamin
,
Qiang Chen
,
Nicholas J. Eagles
,
Louise A. Huuki-Myers
,
Leonardo Collado-Torres
,
Joshua M. Stolz
,
Joo Heon Shin
,
Apuã C.M. Paquola
,
Thomas M. Hyde
,
Joel E. Kleinman
,
Andrew E. Jaffe
,
Shizhong Han †
,
Daniel R. Weinberger †
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Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex
The molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, …
Louise A. Huuki-Myers
,
Abby Spangler
,
Nicholas J. Eagles
,
Kelsey D. Montgomery
,
Sang Ho Kwon
,
Boyi Guo
,
Melissa Grant-Peters
,
Heena R. Divecha
,
Madhavi Tippani
,
Chaichontat Sriworarat
,
Annie B. Nguyen
,
Prashanthi Ravichandran
,
Matthew N. Tran
,
Arta Seyedian
,
PsychENCODE consortium
,
Thomas M. Hyde
,
Joel E. Kleinman
,
Alexis Battle
,
Stephanie C. Page
,
Mina Ryten
,
Stephanie C. Hicks
,
Keri Martinowich
,
Leonardo Collado-Torres †
,
Kristen R. Maynard †
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Code
snRNA-seq code
Documentation
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, …
Chaichontat Sriworarat
,
Annie Nguyen
,
Nicholas J. Eagles
,
Leonardo Collado-Torres
,
Keri Martinowich
,
Kristen R. Maynard †
,
Stephanie C. Hicks †
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Project
DOI
Preprint
Samui Browser
Code
Transcriptional and genetic sex differences for schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus
Schizophrenia is a complex neuropsychiatric disorder with sexually dimorphic features, including differential symptomatology, drug …
Kynon JM Benjamin † __*__
,
Ria Arora __*__
,
Joshua M. Stolz
,
Laura D’Ignazio
,
Leonardo Collado-Torres
,
Thomas M Hyde
,
Joel E Kleinman
,
Daniel R Weinberger †
,
Apuã CM Paquola †
,
Jennifer A Erwin †
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DOI
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VistoSeg: processing utilities for high-resolution Visium/Visium-IF images for spatial transcriptomics data
Background
: Spatial transcriptomics is a next-generation sequencing technology that combines the strengths of transcriptome-wide …
Madhavi Tippani
,
Heena R. Divecha
,
Joseph L. Catallini II
,
Sang Ho Kwon
,
Lukas M. Weber
,
Abby Spangler
,
Andrew E. Jaffe
,
Stephanie C. Hicks
,
Keri Martinowich
,
Leonardo Collado-Torres
,
Stephanie C. Page †
,
Kristen R. Maynard †
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DOI
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Code
Documentation
Data-driven Identification of Total RNA Expression Genes (TREGs) for Estimation of RNA Abundance in Heterogeneous Cell Types
Next-generation sequencing technologies have facilitated data-driven identification of gene sets with different features including …
Louise A. Huuki-Myers
,
Kelsey D. Montgomery
,
Sang Ho Kwon
,
Stephanie C. Page
,
Stephanie C. Hicks
,
Kristen R. Maynard †
,
Leonardo Collado-Torres †
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Project
DOI
Preprint
Code
Documentation
Bioconductor
Source
BiocMAP: A Bioconductor-friendly, GPU-Accelerated Pipeline for Bisulfite-Sequencing Data
Background Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the …
Nicholas J. Eagles
,
Richard Wilton
,
Andrew E. Jaffe
,
Leonardo Collado-Torres
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Code
Documentation
Example analysis
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