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hbcABC

Compilation of rmarkdown templates for bioinformatics analysis

These templates are not ready for fully automatization, it gives a hint about the main figures/tables we produce for specific analysis like chipseq, small-rna, complex rnaseq ... etc

Probably all of them will need some work in some chunks, so don't press knitr button directly without testing the sections.

Installation

if (!require("BiocManager")) {
    install.packages("BiocManager")
}
BiocManager::install("remotes")
BiocManager::install("hbc/bcbioRNASeq")

General tips:

Please go to general_start to get regular tips for all templates.

Templates

  • Index

  • legacy fastrna differential expression: this works with fastrna pipeline using the legacy RNAseq template from Rory's code.

  • Complex differential expression: This template support multiple complex or time serie data. And uses degPattern to cluster genes into expression profiles. It is required to use bcbioRNASeq to create the object.

  • Transcript differential expression with sleuth

  • Singel cell templates: Quick QC, Seurat Clustering analysis with clustree plots.