Man pages for Oscope
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
| AbsCor | Calculate absolute correlations among gene pairs |
| CalcMV | Calculate estimated mean and variance of RNA-Seq data |
| FlagCluster | Flag gene clusters with small within-cluster phase... |
| FormatSineOut | Format SinFun outputs from lists to matrix |
| ImpShift | Search for the optimal sample order by using the Extended... |
| NISFun | Run Extended Nearest Insertion and 2-opt on a gene cluster... |
| NormForSine | Rescale the gene/isoform expression matrix |
| Opt2Shift | Run the 2-opt algorithm to improve the optimal order... |
| OscopeENI | Search for the optimal sample order for different gene... |
| OscopeExampleData | Simulated gene level data set with 600 genes and 30 cells. |
| OscopeKM | Oscope K medoid module |
| Oscope-package | Oscope - A statistical pipeline for identifying oscillatory... |
| OscopeSine | Apply sine model on the full set of genes or isoforms |
| PermuCut | Define sine scroe cutoff using permuted data |
| PipeR | Calculate residual of polynomial fit |
| PipeShiftCDF | Calculate residual of the sliding polynomial regression |
| scanK | Run k-medoid algorithm with varying k on similarity matrix |
| SineFun | Apply sine model on one particular gene vs. other genes |
| SineOptim | Function for searching optimal phase shift |
