Merge branch 'master' of github.com:stemangiola/HCAquery

Author: stemangiola

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: CuratedAtlasQueryR
 Title: Queries the Human Cell Atlas
-Version: 1.1.3
+Version: 1.3.4
 Authors@R: c(
     person(
         "Stefano",
@@ -94,7 +94,8 @@ Imports:
     dbplyr (>= 2.3.0),
     duckdb,
     stringr,
-    checkmate
+    checkmate,
+    stringfish
 Suggests:
     zellkonverter,
     rmarkdown,

NAMESPACE

@@ -6,14 +6,14 @@ export(get_SingleCellExperiment)
 export(get_database_url)
 export(get_default_cache_dir)
 export(get_metadata)
+export(get_pseudobulk)
 export(get_seurat)
 export(get_single_cell_experiment)
 export(get_unharmonised_metadata)
-export(import_metadata_counts)
+export(import_one_sce)
 importFrom(BiocGenerics,cbind)
 importFrom(DBI,dbConnect)
 importFrom(DBI,dbDisconnect)
-importFrom(HDF5Array,HDF5RealizationSink)
 importFrom(HDF5Array,loadHDF5SummarizedExperiment)
 importFrom(HDF5Array,saveHDF5SummarizedExperiment)
 importFrom(S4Vectors,"metadata<-")
@@ -24,7 +24,6 @@ importFrom(SeuratObject,as.Seurat)
 importFrom(SeuratObject,as.sparse)
 importFrom(SingleCellExperiment,"reducedDims<-")
 importFrom(SingleCellExperiment,SingleCellExperiment)
-importFrom(SingleCellExperiment,combineCols)
 importFrom(SingleCellExperiment,reducedDims)
 importFrom(SingleCellExperiment,rowData)
 importFrom(SummarizedExperiment,"assayNames<-")
@@ -80,7 +79,6 @@ importFrom(purrr,reduce)
 importFrom(purrr,set_names)
 importFrom(purrr,walk)
 importFrom(rlang,.data)
-importFrom(stats,setNames)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace_all)