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Hi all. I'd like to introduce the community to shiny_cuffdiff
http://nzgl.github.io/shiny_cuffdiff/
Put simply, this code uses the outputs of the Tuxedo workflow (Tophat2 > Cufflinks > Cuffdiff) which is a cuffdiff SQL database file called cuffdiff.db. Then, using the R package cummeRbund, various plots and outputs are created on-the fly.
shiny_cuffdiff consists of two Shiny apps:
gene_expression_panel_cuffdiff:
Takes a cuffdiff database (rebuilding if required) and displays information on a single named gene (as defined by the gene short name or the XLOC number). After the gene information is defined, gene expression plots can be restricted by sample.
gene_comparison_panel_cuffdiff:
Takes a cuffdiff database (rebuilding if required) and displays information on a set of named genes (as defined by the gene short name or the XLOC number). Displays a heatmap and a barplot. After the gene information is defined, gene expression plots can be restricted by sample.
This project is at an early phase of development, but is under active development.
Participants (either users, testers, or code developers) are encouraged!
We are also developing Shiny code to interrogate the outputs of other common gene expression / differential expression workflows (initially starting with DESeq2), which will be published as a separate repository.
Dan Jones
School of Biological Sciences
The University of Auckland
Please feel free to contact me through SeqAnswers or Github.
This was also posted in the Bioinformatics forum, but I think it is also relevant here. Moderators: feel free to remove this if that's not appropriate.
http://nzgl.github.io/shiny_cuffdiff/
Put simply, this code uses the outputs of the Tuxedo workflow (Tophat2 > Cufflinks > Cuffdiff) which is a cuffdiff SQL database file called cuffdiff.db. Then, using the R package cummeRbund, various plots and outputs are created on-the fly.
shiny_cuffdiff consists of two Shiny apps:
gene_expression_panel_cuffdiff:
Takes a cuffdiff database (rebuilding if required) and displays information on a single named gene (as defined by the gene short name or the XLOC number). After the gene information is defined, gene expression plots can be restricted by sample.
gene_comparison_panel_cuffdiff:
Takes a cuffdiff database (rebuilding if required) and displays information on a set of named genes (as defined by the gene short name or the XLOC number). Displays a heatmap and a barplot. After the gene information is defined, gene expression plots can be restricted by sample.
This project is at an early phase of development, but is under active development.
Participants (either users, testers, or code developers) are encouraged!
We are also developing Shiny code to interrogate the outputs of other common gene expression / differential expression workflows (initially starting with DESeq2), which will be published as a separate repository.
Dan Jones
School of Biological Sciences
The University of Auckland
Please feel free to contact me through SeqAnswers or Github.
This was also posted in the Bioinformatics forum, but I think it is also relevant here. Moderators: feel free to remove this if that's not appropriate.