aggregateRowssupport to reflect internal migration away from Matrix.utils dependency.
spikeNamessupport due to a breaking change in SingleCellExperiment, which has removed
isSpikein favor of
altExps. Refer to the SingleCellExperiment documentation for updated current best practice for handling spike-in transcripts, which now requires slotting a separate SummarizedExperiment object containing things like ERCCs inside the main SingleCellExperiment.
pipeline = "cpi"option is now defunct. Use
pipeline = "none', sheet = 2Lfor CPI samples.
importSampleData: Added optional
autopadZerosargument for easy handling of sample identifiers, which are often input by users without correct padding. This helps easily convert sample_1, sample_2, … sample_10 to expected sample_01, sample_02, … sample_10 sorting. Currently disabled by default.
ignoreGeneVersionoption, now enabled by default. This helps process gene identifiers by default in a manner suitable for downstream tximport-DESeq2 workflow.
headtail: Removed Unicode support in favor of simple ASCII return, to avoid build warnings in latest R 4.0 release version.
DataFrameclass and NCBI server updates.
upperCamelCase: S4 methods for
DataFrameare now defined directly against
DataFrame, instead of attempting to inherit from
DataTablevirtual class. This will break otherwise on bioc-devel 3.12, which seems to have changed inheritance.