bcbioRNASeq

Quality control and differential expression for bcbio RNA-seq experiments.

Installation

This is an R package.

Bioconductor method

source("https://bioconductor.org/biocLite.R")
biocLite(
    "hbc/bcbioRNASeq",
    dependencies = c("Depends", "Imports", "Suggests")
)

Load bcbio run

library(bcbioRNASeq)
bcb <- loadRNASeq(
    uploadDir = file.path("bcbio_rnaseq_run", "final"),
    interestingGroups = c("genotype", "treatment"))

This will return a bcbioRNASeq object, which is an extension of the Bioconductor SummarizedExperiment container class.

Parameters:

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 bcbioRNASeq object. These values should be formatted in camelCase, and can be reassigned in the object after creation (e.g. interestingGroups(bcb) <- c("batch", "age")). They are used for data visualization in the quality control utility functions.

Consult help("loadRNASeq", "bcbioRNASeq") for additional documentation.

This package provides multiple R Markdown templates, including Quality Control and Differential Expression using DESeq2, which are available in RStudio at File -> New File -> R Markdown... -> From Template.

Examples

View example HTML reports rendered from the default R Markdown templates included in the package:

Citation

citation("bcbioRNASeq")

Steinbaugh MJ, Pantano L, Kirchner RD, Barrera V, Chapman BA, Piper ME, Mistry M, Khetani RS, Rutherford KD, Hoffman O, Hutchinson JN, Ho Sui SJ. (2017). bcbioRNASeq: R package for bcbio RNA-seq analysis. F1000Research 6:1976.

References

The papers and software cited in our workflows are available as a shared library on Paperpile.

hliu2016/bcbioRNASeq