Increment version number to 0.5.1.9000

zhanghao-njmu · Oct 9, 2023 · e794a72 · e794a72
1 parent 96e43a2
commit e794a72
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Showing 43 changed files with 3,193 additions and 2,175 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SCP
 Type: Package
 Title: Single Cell Pipeline
-Version: 0.5.1
+Version: 0.5.1.9000
 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.
@@ -14,95 +14,110 @@ Depends:
 biocViews: SingleCell, GeneExpression, SingleCellWorkflow, Visualization, ShinyApps
 Imports:
     AnnotationDbi,
-    BiocParallel,
     biomaRt,
-    ComplexHeatmap (>= 2.13.0),
+    BiocParallel,
     circlize,
     clusterProfiler,
+    ComplexHeatmap (>= 2.13.0),
     data.table,
     dplyr (>= 1.1.0),
     ggnewscale,
     ggplot2 (>= 3.4.0),
-    ggtree (>= 3.6.1),
     ggrepel,
     ggforce,
     GO.db,
     GOSemSim,
     grDevices,
     grid,
-    gridGraphics,
     gtable,
-    gtools,
-    graphics,
+    HDF5Array,
     igraph,
     intrinsicDimension,
-    Matrix (>= 1.5-3),
     methods,
     mgcv,
-    org.Hs.eg.db,
-    org.Mm.eg.db,
-    parallelDist,
+    Matrix,
     patchwork,
     png,
+    plotly,
     proxyC,
     R.cache,
     R.utils,
-    Rcpp,
     reshape2,
     reticulate,
     rlang,
-    Signac,
-    Seurat (>= 4.2.0),
-    SeuratObject,
+    rhdf5,
     scales,
     simplifyEnrichment (>= 1.5.2),
     slingshot,
+    Signac,
+    Seurat (>= 4.2.0),
+    SeuratObject,
     uwot
-Remotes:
-    jokergoo/ComplexHeatmap,
-    jokergoo/simplifyEnrichment,
-    YuLab-SMU/ggtree
 Suggests:
     AUCell,
+    batchelor,
+    Biobase,
+    BiocGenerics,
+    BiocManager,
     concaveman,
+    conos,
     covr,
+    cowplot,
+    dendextend,
     destiny,
     devtools,
+    DDRTree,
+    e1071,
     future,
-    ggupset,
+    ggpubr,
+    ggridges,
     ggsignif,
-    ggwordcloud,
+    ggupset,
     ggVennDiagram,
+    ggwordcloud,
     glmGamPoi,
+    glmpca,
+    harmony,
     hexbin,
     htmlwidgets,
     httr,
-    HDF5Array,
-    MASS,
-    Mfuzz,
     metR,
     monocle,
+    monocle3,
+    MatrixGenerics,
+    MASS,
     NMF,
-    plotly,
+    openxlsx,
+    org.Hs.eg.db,
+    org.Mm.eg.db,
     promises,
-    RcppParallel,
-    RcppML,
+    purrr,
+    PFAM.db,
+    ragg,
+    reactome.db,
     renv,
-    rhdf5,
     rliger,
-    S4Vectors,
+    RcppParallel,
+    RcppML,
     scattermore,
     scds,
     scDblFinder,
     scmap,
+    sf,
     shiny (>= 1.6.0),
     styler,
+    stringr,
     sva,
+    symphony,
+    S4Vectors,
     SingleR,
-    ragg,
+    SingleCellExperiment,
+    SummarizedExperiment,
     testthat (>= 3.0.0),
+    tidyr,
+    umap,
     UCell,
-    umap
+    withr
 LinkingTo: Rcpp
 RoxygenNote: 7.2.3
 Config/testthat/edition: 3

diff --git a/NAMESPACE b/NAMESPACE
@@ -31,6 +31,8 @@ S3method(drop_data,patchwork)
 S3method(slim_data,default)
 S3method(slim_data,ggplot)
 S3method(slim_data,patchwork)
+export("%>%")
+export("%||%")
 export(AnnotateFeatures)
 export(BBKNN_integrate)
 export(CC_GenePrefetch)
@@ -108,7 +110,6 @@ export(RunSymphonyMap)
 export(RunTriMap)
 export(RunUMAP2)
 export(RunWOT)
-export(SankeyPlot)
 export(Scanorama_integrate)
 export(Seurat_integrate)
 export(SrtAppend)
@@ -126,7 +127,6 @@ export(capitalize)
 export(check_DataType)
 export(check_Python)
 export(check_R)
-export(check_python_element)
 export(check_srtList)
 export(check_srtMerge)
 export(compute_velocity_on_grid)
@@ -168,6 +168,10 @@ export(theme_scp)
 export(tochunks)
 export(try_get)
 export(unnest)
+importFrom(AnnotationDbi,columns)
+importFrom(AnnotationDbi,keys)
+importFrom(AnnotationDbi,mappedkeys)
+importFrom(AnnotationDbi,select)
 importFrom(BiocParallel,"bpRNGseed<-")
 importFrom(BiocParallel,"bpprogressbar<-")
 importFrom(BiocParallel,SerialParam)
@@ -199,6 +203,9 @@ importFrom(ComplexHeatmap,restore_matrix)
 importFrom(ComplexHeatmap,row_order)
 importFrom(ComplexHeatmap,width.HeatmapAnnotation)
 importFrom(ComplexHeatmap,width.Legends)
+importFrom(HDF5Array,TENxMatrix)
+importFrom(HDF5Array,writeTENxMatrix)
+importFrom(Matrix,Matrix)
 importFrom(Matrix,colMeans)
 importFrom(Matrix,colSums)
 importFrom(Matrix,rowMeans)
@@ -293,6 +300,7 @@ importFrom(circlize,circos.clear)
 importFrom(circlize,colorRamp2)
 importFrom(clusterProfiler,GSEA)
 importFrom(clusterProfiler,enricher)
+importFrom(clusterProfiler,read.gmt)
 importFrom(clusterProfiler,simplify)
 importFrom(data.table,fread)
 importFrom(data.table,rbindlist)
@@ -331,6 +339,7 @@ importFrom(ggplot2,annotation_custom)
 importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,coord_polar)
+importFrom(ggplot2,cut_number)
 importFrom(ggplot2,draw_key_point)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_line)
@@ -425,14 +434,16 @@ importFrom(ggplot2,wrap_dims)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(ggplot2,zeroGrob)
+importFrom(ggrepel,GeomTextRepel)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRamp)
 importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,dev.control)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,png)
+importFrom(grDevices,recordPlot)
 importFrom(grDevices,rgb)
-importFrom(graphics,par)
-importFrom(graphics,rect)
-importFrom(graphics,text)
 importFrom(grid,addGrob)
 importFrom(grid,arrow)
 importFrom(grid,convertHeight)
@@ -459,7 +470,6 @@ importFrom(grid,unit)
 importFrom(grid,unit.pmax)
 importFrom(grid,unitType)
 importFrom(grid,viewport)
-importFrom(gridGraphics,echoGrob)
 importFrom(gtable,gtable)
 importFrom(gtable,gtable_add_cols)
 importFrom(gtable,gtable_add_grob)
@@ -498,14 +508,27 @@ importFrom(methods,getFunction)
 importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
-importFrom(parallelDist,parDist)
 importFrom(patchwork,wrap_plots)
+importFrom(plotly,add_trace)
+importFrom(plotly,as_widget)
+importFrom(plotly,layout)
+importFrom(plotly,plot_ly)
+importFrom(proxyC,dist)
+importFrom(proxyC,simil)
 importFrom(reshape2,dcast)
 importFrom(reshape2,melt)
 importFrom(reticulate,import)
 importFrom(reticulate,iterate)
 importFrom(reticulate,np_array)
 importFrom(reticulate,py_to_r)
+importFrom(rhdf5,h5createDataset)
+importFrom(rhdf5,h5createFile)
+importFrom(rhdf5,h5createGroup)
+importFrom(rhdf5,h5delete)
+importFrom(rhdf5,h5ls)
+importFrom(rhdf5,h5read)
+importFrom(rhdf5,h5readAttributes)
+importFrom(rhdf5,h5write)
 importFrom(rlang,"%||%")
 importFrom(rlang,call2)
 importFrom(rlang,caller_env)
@@ -526,13 +549,13 @@ importFrom(stats,as.dendrogram)
 importFrom(stats,as.dist)
 importFrom(stats,binom.test)
 importFrom(stats,cmdscale)
-importFrom(stats,dist)
 importFrom(stats,formula)
 importFrom(stats,hclust)
 importFrom(stats,kmeans)
 importFrom(stats,loess)
 importFrom(stats,mad)
 importFrom(stats,median)
+importFrom(stats,model.matrix)
 importFrom(stats,na.omit)
 importFrom(stats,order.dendrogram)
 importFrom(stats,p.adjust)