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.
geneNamecolumns. Use corresponding
makeProtein2GeneFromEnsemblto generate object simplify using Ensembl protein IDs as input.
getEnsDb: Now exporting function that was used internally to obtain
EnsDbobject from AnnotationHub.
makeProtein2GeneFromEnsembl: New utility function that takes Ensembl protein identifiers as input, and returns corresponding gene identifiers and gene names (i.e. HUGO gene symbols).
makeGRangesFromEnesmblto enable export of new
getEnsDb: Improved sorting of Ensembl releases so that current release greater than 99 returns as expected. Since Ensembl is now at 101, we need to convert to integers internally instead of attempting to sort on strings.