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.
if (!require("BiocManager")) {
install.packages("BiocManager")
}
BiocManager::install("remotes")
BiocManager::install("hbc/bcbioRNASeq")
Please go to general_start to get regular tips for all templates.
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.
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