SPECK
Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding
Description
Surface Protein abundance Estimation using CKmeans-based clustered thresholding ('SPECK') is an unsupervised learning-based method that performs receptor abundance estimation for single cell RNA-sequencing data based on reduced rank reconstruction (RRR) and a clustered thresholding mechanism. Seurat's normalization method is described in: Hao et al., (2021) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for the RRR is further detailed in: Erichson et al., (2019) <doi:10.18637/jss.v089.i11> and Halko et al., (2009) <doi:10.48550/arXiv.0909.4061>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.
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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 | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| 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 History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Package required but not available: ‘Seurat’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 30, 2026
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 4.8Mb
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 4.8Mb
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'SPECKVignette.Rmd' using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| *************************** ...[truncated]... i.org/tinytex/r/#debugging for debugging tips. See SPECKVignette.log for more info. --- failed re-building 'SPECKVignette.Rmd' SUMMARY: processing the following file failed: 'SPECKVignette.Rmd' Error: Vignette re-building failed. Execution halted
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 4.8Mb
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 4.8Mb