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Reproducible RNA-seq analysis using recount2 | L. Collado-Torres
lcolladotor.github.iorecount2 is a resource of processed and summarized expression data spanning over 70,000 human RNA-seq samples from the Sequence Read Archive (SRA). The associated recount Bioconductor package provides a convenient API for querying, downloading, and analyzing the data. Each processed study consists of meta/phenotype data, the expression levels of genes and their underlying exons and splice junctions, and corresponding genomic annotation. We also provide data summarization types for quantifying novel transcribed sequence including base-resolution coverage and potentially unannotated splice junctions. We present workflows illustrating how to use recount to perform differential expression analysis including meta-analysis, annotation-free base-level analysis, and replication of smaller studies using data from larger studies. recount provides a valuable and user-friendly resource of processed RNA-seq datasets to draw additional biological insights from existing public data. The resource is available at https://jhubiostatistics.shinyapps.io/recount/.
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| Title | Reproducible RNA-seq analysis using recount2 | L. Collado-Torres | ||||||||||||||||||||||||||||||||||||
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| Keywords cloud | data expression RNAseq recount processed resource analysis junctions splice studies Bioconductor recount2 including ColladoTorres thoughts replication × biological additional draw | ||||||||||||||||||||||||||||||||||||
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Internal links in - lcolladotor.github.io
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
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recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]
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recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations] | L. Collado-Torres
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Lcolladotor.github.io Spined HTML
Reproducible RNA-seq wringer using recount2 | L. Collado-Torres Toggle navigation L. Collado-Torres Home Publications Talks Blog CV Students Teaching Contact Search Reproducible RNA-seq wringer using recount2 L Collado-Torres *, A Nellore *, K Kammers, SE Ellis, MA Taub, KD Hansen, AE Jaffe, B Langmead, JT Leek Abstract recount2 is a resource of processed and summarized expression data spanning over 70,000 human RNA-seq samples from the Sequence Read Archive (SRA). The associated recount Bioconductor package provides a user-friendly API for querying, downloading, and analyzing the data. Each processed study consists of meta/phenotype data, the expression levels of genes and their underlying exons and splice junctions, and respective genomic annotation. We moreover provide data summarization types for quantifying novel transcribed sequence including base-resolution coverage and potentially unannotated splice junctions. We present workflows illustrating how to use recount to perform differential expression wringer including meta-analysis, annotation-free base-level analysis, and replication of smaller studies using data from larger studies. recount provides a valuable and user-friendly resource of processed RNA-seq datasets to yank spare biological insights from existing public data. The resource is misogynist at https://jhubiostatistics.shinyapps.io/recount/. Type Peer-reviewed Publication Nature Biotechnology Date April, 2017 Links PDF Code Project Bioconductor Pre-print © 2011-2018 Leonardo Collado Torres under (CC) BY-NC-SA 4.0. All thoughts and opinions here are my own. · Powered by the Academic theme for Hugo. × Cite Copy Download