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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Summary SpatialExperiment is a new data infrastructure for storing and accessing spatially resolved transcriptomics data, implemented …
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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways
Recent genetic studies have identified variants associated with bipolar disorder (BD), but it remains unclear how brain gene expression …
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Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways
Genetics and Brain Transcriptomics of Completed Suicide
Objective: The authors sought to study the transcriptomic and genomic features of completed suicide by parsing the method chosen, to …
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recount3: summaries and queries for large-scale RNA-seq expression and splicing
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples …
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recount3: summaries and queries for large-scale RNA-seq expression and splicing
Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain
Single-cell gene expression technologies are powerful tools to study cell types in the human brain, but efforts have largely focused on …
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Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain
Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk
DNA methylation (DNAm) is an epigenetic regulator of gene expression and a hallmark of gene-environment interaction. Using whole-genome …
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Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/Bioconductor-powered RNA-seq analyses
Background. RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with …
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SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/Bioconductor-powered RNA-seq analyses
Developmental Profile of Psychiatric Risk Associated With Voltage-Gated Cation Channel Activity
Background. Recent breakthroughs in psychiatric genetics have implicated biological pathways onto which genetic risk for psychiatric …
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Developmental Profile of Psychiatric Risk Associated With Voltage-Gated Cation Channel Activity
Megadepth: efficient coverage quantification for BigWigs and BAMs
Motivation. A common way to summarize sequencing datasets is to quantify data lying within genes or other genomic intervals. This can …
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Megadepth: efficient coverage quantification for BigWigs and BAMs
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
We used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral …
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Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex