diff --git a/DESCRIPTION b/DESCRIPTION index f007a23..62c7d65 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SingleR Title: Reference-Based Single-Cell RNA-Seq Annotation -Version: 2.9.0 -Date: 2024-10-28 +Version: 2.9.1 +Date: 2024-11-17 Authors@R: c(person("Dvir", "Aran", email="dvir.aran@ucsf.edu", role=c("aut", "cph")), person("Aaron", "Lun", email="infinite.monkeys.with.keyboards@gmail.com", role=c("ctb", "cre")), person("Daniel", "Bunis", role="ctb"), diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 4c7c6bc..64f7daf 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -2,6 +2,14 @@ \title{SingleR News} \encoding{UTF-8} +\section{Version 2.10.0}{\itemize{ +\item Switch to \pkg{scrapper} for DE detection when \code{de.method="t"} or \code{de.method="wilcox"} in \code{trainSingleR()}. +This should give similar results to but is faster than the previous \pkg{scran} functions. + +\item Switch to \pkg{scrapper} for variance calculation, PCA and clustering in \code{aggregateReference()}. +This should be faster than the previous \pkg{BiocSingular} and \code{stats::kmeans} functions, and avoids the need to consider the seed. +}} + \section{Version 2.8.0}{\itemize{ \item Added the \code{test.genes=} argument to \code{trainSingleR()}, to restrict marker detection to only those genes in the test dataset. This is also checked against \code{rownames(test)} in \code{classifySingleR()} to ensure that the test's feature space is consistent with the space used during training.