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Biologist-intelligible alternative splicing analysis of RNA-seq data. Barbosa-Morais, Nuno Luis
Description
I will give an overview of our labâ s efforts on making the analysis of alternative splicing from RNA-seq datasets more intuitive and informative to biologists. I will introduce psichomics, a modular and extensible Bioconductor package with an intuitive Shiny-based graphical interface for alternative splicing quantification and downstream dimensionality reduction, differential splicing and gene expression and survival analyses based on The Cancer Genome Atlas, the Genotype-Tissue Expression, and the Sequence Read Archive (via recount2) projects, as well as user-provided data. These integrative analyses can incorporate clinical and molecular sample-associated features and be performed on a laptop. I will also discuss how Beta distributions can be exploited in modeling exon inclusion levels, incorporating information about the coverage-associated precision of their estimates by using the numbers of reads supporting exon inclusion and exclusion as surrogates of the distributionâ s shape parameters. Beta distributions provide a sensible framework for differential splicing analysis of small sample size datasets.
Item Metadata
Title |
Biologist-intelligible alternative splicing analysis of RNA-seq data.
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Creator | |
Publisher |
Banff International Research Station for Mathematical Innovation and Discovery
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Date Issued |
2018-11-06T12:08
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Description |
I will give an overview of our labâ s efforts on making the analysis of alternative splicing from RNA-seq datasets more intuitive and informative to biologists.
I will introduce psichomics, a modular and extensible Bioconductor package with an intuitive Shiny-based graphical interface for alternative splicing quantification and downstream dimensionality reduction, differential splicing and gene expression and survival analyses based on The Cancer Genome Atlas, the Genotype-Tissue Expression, and the Sequence Read Archive (via recount2) projects, as well as user-provided data. These integrative analyses can incorporate clinical and molecular sample-associated features and be performed on a laptop.
I will also discuss how Beta distributions can be exploited in modeling exon inclusion levels, incorporating information about the coverage-associated precision of their estimates by using the numbers of reads supporting exon inclusion and exclusion as surrogates of the distributionâ s shape parameters. Beta distributions provide a sensible framework for differential splicing analysis of small sample size datasets.
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Extent |
28.0
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Subject | |
Type | |
File Format |
video/mp4
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Language |
eng
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Notes |
Author affiliation: Instituto de Medicina Molecular João Lobo Antunes
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Series | |
Date Available |
2019-05-06
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Provider |
Vancouver : University of British Columbia Library
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Rights |
Attribution-NonCommercial-NoDerivatives 4.0 International
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DOI |
10.14288/1.0378593
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URI | |
Affiliation | |
Peer Review Status |
Unreviewed
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Scholarly Level |
Other
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Rights URI | |
Aggregated Source Repository |
DSpace
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Item Citations and Data
Rights
Attribution-NonCommercial-NoDerivatives 4.0 International