Merge pull request #204 from zhanghao-njmu/develop

Develop

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SCP
 Type: Package
 Title: Single Cell Pipeline
-Version: 0.5.4
+Version: 0.5.5
 Author: Hao Zhang
 Maintainer: Hao Zhang <[email protected]>
 Description: An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
@@ -21,6 +21,8 @@ Imports:
     ComplexHeatmap (>= 2.13.0),
     data.table,
     dplyr (>= 1.1.0),
+    future,
+    future.apply,
     ggnewscale,
     ggplot2 (>= 3.4.0),
     ggrepel,
@@ -37,6 +39,7 @@ Imports:
     mgcv,
     Matrix,
     patchwork,
+    pbapply,
     png,
     plotly,
     proxyC,
@@ -68,7 +71,6 @@ Suggests:
     devtools,
     DDRTree,
     e1071,
-    future,
     ggpubr,
     ggridges,
     ggsignif,

NAMESPACE

@@ -57,6 +57,7 @@ export(FeatureDimPlot3D)
 export(FeatureHeatmap)
 export(FeatureStatPlot)
 export(FetchH5)
+export(FindExpressedMarkers)
 export(GSEAPlot)
 export(GeneConvert)
 export(GraphPlot)
@@ -206,6 +207,7 @@ importFrom(ComplexHeatmap,width.Legends)
 importFrom(HDF5Array,TENxMatrix)
 importFrom(HDF5Array,writeTENxMatrix)
 importFrom(Matrix,Matrix)
+importFrom(Matrix,as.matrix)
 importFrom(Matrix,colMeans)
 importFrom(Matrix,colSums)
 importFrom(Matrix,rowMeans)
@@ -228,6 +230,7 @@ importFrom(Seurat,Assays)
 importFrom(Seurat,AverageExpression)
 importFrom(Seurat,CaseMatch)
 importFrom(Seurat,Cells)
+importFrom(Seurat,Command)
 importFrom(Seurat,CreateAssayObject)
 importFrom(Seurat,CreateDimReducObject)
 importFrom(Seurat,CreateSeuratObject)
@@ -327,6 +330,8 @@ importFrom(dplyr,reframe)
 importFrom(dplyr,slice_head)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_at)
+importFrom(future,nbrOfWorkers)
+importFrom(future.apply,future_sapply)
 importFrom(ggforce,geom_mark_ellipse)
 importFrom(ggforce,geom_mark_hull)
 importFrom(ggnewscale,new_scale)
@@ -511,6 +516,7 @@ importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
 importFrom(patchwork,wrap_plots)
+importFrom(pbapply,pbsapply)
 importFrom(plotly,add_trace)
 importFrom(plotly,as_widget)
 importFrom(plotly,layout)