Merge pull request #7565 from satijalab/ParseUpdate

update ReadParseBio to be compatible with latest split-pipe v1.1.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.3.0.9008
-Date: 2023-07-06
+Version: 4.3.0.9009
+Date: 2023-07-12
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(

NEWS.md

@@ -6,6 +6,7 @@
 - Fix fold change calculation for assays ([#739](https://github.com/satijalab/seurat-private/pull/739))
 - Fix `pt.size` bug when rasterization is set to true ([#7379](https://github.com/satijalab/seurat/issues/7379)) 
 - Fix `FoldChange` and `FindMarkers` to support all normalization approaches ([#7115](https://github.com/satijalab/seurat/pull/7115),[#7110](https://github.com/satijalab/seurat/issues/7110),[#7095](https://github.com/satijalab/seurat/issues/7095),[#6976](https://github.com/satijalab/seurat/issues/6976),[#6654](https://github.com/satijalab/seurat/issues/6654),[#6701](https://github.com/satijalab/seurat/issues/6701),[#6773](https://github.com/satijalab/seurat/issues/6773), [#7107](https://github.com/satijalab/seurat/issues/7107))
+- Fix for handling newer ParseBio formats in `ReadParseBio` ([#7565](https://github.com/satijalab/seurat/pull/7565))
 
 # Seurat 4.3.0 (2022-11-18)
 

R/convenience.R

@@ -391,7 +391,8 @@ SpecificDimPlot <- function(object, ...) {
 #' @export
 #'
 ReadParseBio <- function(data.dir, ...) {
-  mtx <- file.path(data.dir, "DGE.mtx")
+  file.dir <- list.files(path = data.dir, pattern = ".mtx")
+  mtx <- file.path(data.dir, file.dir)
   cells <- file.path(data.dir, "cell_metadata.csv")
   features <- file.path(data.dir, "all_genes.csv")
   return(ReadMtx(