Man pages for ramiromagno/oscillation
A Statistical Pipeline for Identifying Oscillatory Genes in Unsynchronized Single Cell RNA-Seq
| CalcMV | Calculate estimated mean and variance of RNA-Seq data |
| filter_by_mean_count | Filter genes by mean counts |
| find_optimal_phase_shift | Optimal phase shift |
| FlagCluster | Flag gene clusters with small within-cluster phase... |
| FormatSineOut | Format SinFun outputs from lists to matrix |
| gene_statistics | Gene expression statistics |
| gm_mean | Geometric mean |
| ImpShift | Search for the optimal sample order by using the Extended... |
| mean_variance_fit | Linear regression on gene variance and mean |
| median2 | Median over positive values |
| median_norm_size_factors | Median normalisation size factors |
| median_norm_size_factors2 | Median normalisation size factors (alternative) |
| 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 |
| paired_sine_analysis | Perform paired-sine mode analysis |
| PermuCut | Define sine scroe cutoff using permuted data |
| pipe | Pipe operator |
| PipeR | Calculate residual of polynomial fit |
| PipeShiftCDF | Calculate residual of the sliding polynomial regression |
| pseudo_ref_sample | Calculate the pseudo-reference sample |
| read_gsm_as_matrix | Reads a GEO GSM (.csv or .csv.gz) file |
| scanK | Run k-medoid algorithm with varying k on similarity matrix |
| score_matrix | Converts the data frame of paired-sine scores to a matrix |
| SineFun | Apply sine model on one particular gene vs. other genes |
| SineOptim | Function for searching optimal phase shift |
| squared_epsilon | Paired-sine model squared error term |
