scDiagnostics
Diagnostic functions for assessing the quality of cell type annotations in single-cell RNA-seq data. Developed at the Core for Computational Biomedicine, Harvard Medical School.
Software
Software
R packages, distributed through Bioconductor and CRAN. Seven have C++ backends.
15Packages
684,944CRAN downloads
7C++ backends
2018First release
Bioconductor
scDiagnosticsApp
An interactive interface to scDiagnostics. The application can be deployed locally from source, or accessed through the hosted instance at Harvard Medical School.
Ensembles, subset selection and robust regression 10 packages
| Package | Description | Version | Downloads | Links |
|---|---|---|---|---|
| srlars | Fast and scalable cellwise-robust ensembles, built on a Detect Deviating Cells foundation. | 3.1.0 | 7,941 | CRAN Source |
| RMSS | Robust multi-model subset selection. | 1.2.4 | 8,412 | CRAN Source C++ |
| PSGD | GLM ensembles via a projected subset gradient descent algorithm. | 1.0.6 | 12,191 | CRAN Source C++ |
| CPGLIB | Ensembles of GLMs using competing proximal gradients. Linear and logistic models. | 1.1.2 | 18,989 | CRAN Source |
| SplitGLM | Split GLMs via block coordinate descent. Linear, logistic, Poisson and Gamma models. | 1.0.6 | 17,672 | CRAN Source |
| SplitReg | Split regularized regression. | 1.0.3 | 22,309 | CRAN Source |
| robStepSplitReg | Robust stepwise split regularized regression. | 2.0.0 | 9,401 | CRAN Source |
| stepSplitReg | Stepwise split regularized regression. | 1.0.5 | 13,003 | CRAN Source |
| splitSelect | Best split selection modeling for low-dimensional data. | 1.0.3 | 22,021 | CRAN Source |
| nnGarrote | Non-negative garrote estimation with penalized initial estimators. | 1.0.4 | 25,563 | CRAN Source |
Risk and performance estimation 3 packages
| Package | Description | Version | Downloads | Links |
|---|---|---|---|---|
| RPESE | Standard errors for risk and performance measures with serially dependent data. | 1.2.7 | 203,599 | CRAN Source |
| RPEIF | Computation and plots of influence functions for risk and performance measures. | 1.2.5 | 156,244 | CRAN Source |
| RPEGLMEN | Gamma and exponential GLMs with an elastic net penalty, fitted with FISTA. | 1.1.4 | 148,855 | CRAN Source |
Utilities 1 package
| Package | Description | Version | Downloads | Links |
|---|---|---|---|---|
| simTargetCov | Transform or simulate data with a target empirical covariance matrix. | 1.0.1 | 18,744 | CRAN Source |
Versions and download counts are current as of 27 September 2026. Download counts are RStudio CRAN mirror
totals and reflect one mirror only.
GitHub