Man pages for ttdtrang/gbnorm
Graph-based Normalization of RNA-seq data
| build.graph | Build graph from correlation matrix |
| cdev | Condition-number-based deviation of X and Y, assuming X can... |
| cdev.generic | Condition-number-based deviation of X and Y, for generally... |
| community.cut | Community cut |
| community.gce | Community detection by GCE |
| community.shell | community.shell |
| community.strength.internal | Community internal strength |
| community.volume | Community volume |
| crossval | generic function for cross-validation |
| cv.lognorm | Coefficient of variation, unbiased estimate for log-normal... |
| fast.condNumber | Condition number using fast.svd |
| geom.mean | Geometric mean |
| get.references.apcluster | get.references.apcluster |
| get.references.blocks | Identify the best set of references |
| get.references.dbscan | get.references.dbscan |
| get.references.hclust | get.references.hclust |
| get.references.v1 | get.references |
| linspace | linspace |
| measure.M | calculate M measure, defined as |
| normalize.by.deges | Normalize by DEGES |
| normalize.by.deseq | Call estimateSizeFactorsForMatrix by DESeq2 |
| normalize.by.poissonseq | Normalize by PoissonSeq |
| normalize.by.refs | Normalizing (global-scaling) using references |
| normalize.by.ruv_r | Normalize by RUVr |
| normalize.by.scaleFactors | normalize.by.scaleFactors |
| normalize.by.tmm | Call calcNormFactors by edgeR |
| normalize.by.uq | Normalize by Upper Quantile |
| rank1.residuals | the magnitude of the singular values except the first one |
| rmsd | Least root mean square distance between two set of points in... |
| simulate.counts | simulate.counts |
| srms | Standardized root mean squared deviation between two matrices |
| variance.refs | variance.refs |
