scRNAstat
A Pipeline to Process Single Cell RNAseq Data
Description
A pipeline that can process single or multiple Single Cell RNAseq samples primarily specializes in Clustering and Dimensionality Reduction. Meanwhile we use common cell type marker genes for T cells, B cells, Myeloid cells, Epithelial cells, and stromal cells (Fiboblast, Endothelial cells, Pericyte, Smooth muscle cells) to visualize the Seurat clusters, to facilitate labeling them by biological names. Once users named each cluster, they can evaluate the quality of them again and find the de novo marker genes also.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (2 non-OK)
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
Check History
NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
ERROR 10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Packages required but not available: 'Seurat', 'clustree' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 20, 2026
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘DBI’ ‘colorspace’ All declared Imports should be used.
WARNING 11 OK · 0 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE Apr 23, 2026
namespace references in data files
Data files with namespace references not in the recursive strong package dependencies: data/AJ064_small_last_sce.rda: colorspace DBI See section 'Data in packages' in the 'Writing R Extensions' manual.
namespace references in data files
Data files with namespace references not in the recursive strong package dependencies: data/AJ064_small_last_sce.rda: colorspace DBI See section 'Data in packages' in the 'Writing R Extensions' manual.
namespace references in data files
Data files with namespace references not in the recursive strong package dependencies: data/AJ064_small_last_sce.rda: colorspace DBI See section 'Data in packages' in the 'Writing R Extensions' manual.
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 10, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 9, 2026
package dependencies
Package required but not available: ‘Seurat’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.