Quality control and differential expression for bcbio RNA-seq experiments.
This is an R package.
Ensure that these dependencies install correctly:
biocLite(c( "steinbaugh/basejump", "lpantano/DEGreport", "tidyverse", "rmarkdown", "knitr", "formatR", "GenomeInfoDbData" ))
Now you’re ready to install bcbioRNASeq:
For the Functional Analysis R Markdown template, these additional libraries are required:
biocLite(c( "clusterProfiler", "DOSE", "pathview" ))
library(bcbioRNASeq) bcb <- loadRNASeq( uploadDir = file.path("bcbio_rnaseq_run", "final"), interestingGroups = c("genotype", "treatment"))
uploadDir: Path to the bcbio final upload directory.
interestingGroups: Character vector of the column names of interest in the sample metadata, which is stored in the
colData()accessor slot of the
bcbioRNASeqobject. These values should be formatted in camelCase, and can be reassigned in the object after creation (e.g.
metadata(bcb)$interestingGroups <- c("batch", "age")). They are used for data visualization in the quality control utility functions.
help("loadRNASeq", "bcbioRNASeq") for additional documentation.
This package provides multiple RMarkdown templates, including Quality Control and Differential Expression using DESeq2, which are available in RStudio at
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