- Import directly from DelayedArray, as this seems to be necessary: rowSums colSums rowMeans colMeans
- No longer import from BiocGenerics (not needed any more?): rowSums colSums rowMeans colMeans
- Add option do_logNormCounts, and try to not error-out on completely empty cells.
- Default to unstranded gaps (i.e. don't extend into gene on opposite strand).
- peak_min_prop added, default 0.01, removes sites with a proportionately low total count from genes.
- computeSumFactors is done using quickCluster, with quickCluster blocked by batch, sizeFactors only computed once (gene level).
- Various changes aiming to reduce memory usage.