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


This is an R package.

Bioconductor method

    dependencies = c("Depends", "Imports", "Suggests")

conda method

conda install -c bioconda r-bcbiornaseq

Load bcbio run

bcb <- bcbioRNASeq(
    uploadDir = "bcbio_rnaseq_run/final",
    interestingGroups = c("genotype", "treatment"),
    organism = "Homo sapiens"
# Back up all data inside bcbioRNASeq object
flatFiles <- flatFiles(bcb)
saveData(bcb, flatFiles)

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


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

Sample metadata

When loading a bcbio RNA-seq run, the sample metadata will be imported automatically from the project-summary.yaml file in the final upload directory. If you notice any typos in your metadata after completing the run, these can be corrected by editing the YAML file. Alternatively, you can pass in a sample metadata file into bcbioRNASeq() using the sampleMetadataFile argument.

Metadata file example

The samples in the bcbio run must map to the description column. The values provided in description must be unique. These values will be sanitized into syntactically valid names (see help("makeNames", "basejump")), and assigned as the column names of the bcbioRNASeq object. The original values are stored as the sampleName column in colData(), and are used for all plotting functions.

| description | genotype | |-------------|----------| | sample1 | wildtype | | sample2 | knockout | | sample3 | wildtype | | sample4 | knockout |

R Markdown templates

This package provides multiple R Markdown templates, including quality control, differential expression using DESeq2, and functional enrichment analysis.

These are available in RStudio at File -> New File -> R Markdown... -> From Template.

Example renderings



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.


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

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.