bcbioSingleCell

NOTE: bcbio-nextgen is no longer under active development. Refer to the notice of discontinuation for additional details.

R package for bcbio single-cell RNA-seq analysis.

Installation

This is an R package.

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
install.packages(
    pkgs = "bcbioSingleCell",
    repos = c(
        "https://r.acidgenomics.com",
        BiocManager::repositories()
    ),
    dependencies = TRUE
)

Conda method

Configure Conda to use the Bioconda channels.

# Don't install recipe into base environment.
conda create --name='r-bcbiosinglecell' 'r-bcbiosinglecell'
conda activate 'r-bcbiosinglecell'
R

Load bcbio single-cell RNA-seq data

library(bcbioSingleCell)
object <- bcbioSingleCell(
    uploadDir = file.path("indrops", "final"),
    interestingGroups = c("genotype", "treatment"),
    sampleMetadataFile = "sample_metadata.csv",
    organism = "Homo sapiens",
    ensemblRelease = 90L
)

This will return a bcbioSingleCell object, which is an extension of the Bioconductor SingleCellExperiment container class. Consult the bcbioSingleCell() constructor function documentation for detailed information on the supported parameters:

help(topic = "bcbioSingleCell", package = "bcbioSingleCell")

Sample metadata examples

FASTQ files with samples multiplexed by index barcode

This is our current recommended method for analyzing an inDrops dataset. The sample index barcodes are multiplexed per FASTQ set. For Illumina sequencing data, the raw binary base call (BCL) data must be converted into FASTQs (split into R1-R4 files) using bcl2fastq.

The inDrops library version is automatically detected by bcbio, but ensure that the sample index sequences provided match the library version when attempting to create a bcbioSingleCell object.

Consult the bcbio documentation for more information on how to configure an inDrops run prior to loading into R with the bcbioSingleCell() function.

description	index	sequence	sampleName	aggregate	genotype
indrops1	1	CTCTCTAT	sample1_1	sample1	wildtype
indrops1	2	TATCCTCT	sample2_1	sample2	knockout
indrops1	3	GTAAGGAG	sample3_1	sample3	wildtype
indrops1	4	ACTGCATA	sample4_1	sample4	knockout
indrops2	1	CTCTCTAT	sample1_2	sample1	wildtype
indrops2	2	TATCCTCT	sample1_2	sample2	knockout
indrops2	3	GTAAGGAG	sample1_2	sample3	wildtype
indrops2	4	ACTGCATA	sample1_2	sample4	knockout

Note that bcbio currently outputs the reverse complement index sequence in the sample directory names (e.g. sample-ATAGAGAG). Define the forward index barcode in the sequence column here, not the reverse complement. The reverse complement will be calculated automatically and added as the revcomp column in the sample metadata.

FASTQ files demultiplexed per sample

This is our current method for handling 10X Genomics Chromium and Illumina SureCell cell barcodes.

description	genotype
sample1	wildtype
sample2	knockout
sample3	wildtype
sample4	knockout

Invalid object

If you encounter a validObject error when attempting to load a bcbioSingleCell object from a previous analysis, run this step to update the object to the current version of the package:

object <- updateObject(object)
validObject(object)
## [1] TRUE

References

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