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. (2018). bcbioRNASeq: R package for bcbio RNA-seq analysis. F1000Research 6:1976.
We recommend installing the package with BiocManager.
To avoid version issues, your
.condarc file should only contain the following channels, in this order:
channels: - conda-forge - bioconda - defaults
We recommend installing into a clean conda environment:
Now you’re ready to install
This will return a
bcbioRNASeq object, which is an extension of the Bioconductor RangedSummarizedExperiment container class. Consult the
bcbioRNASeq() constructor function documentation for detailed information on the supported parameters:
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
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.
These are available in RStudio at
New File ->
R Markdown... ->