Man pages for wjawaid/bglab
Berthold Gottgens lab scRNA seq
| addPath | Store path |
| addPath-reducedDim-method | Store path |
| addPath-SCD-method | Store path |
| addPheno | Add additional phenotype data |
| addPheno-SCD-method | Add additional phenotype data |
| applyGaussianKernelwithVariableSigma | Apply Gaussian Kernel using Laleh Haghverdi's variable sigma |
| applyMVP | Applies transformation from rgl plot to data |
| bglab | Gottgens Lab Toolkit |
| clipboard | Copy R content to clipboard |
| clustLouvain | Perform Louvain clustering |
| colorGradient | Helper function for 'plotGene' |
| counts-SCD-method | Retrieve counts data from Single Cell Dataset object |
| diffuse | Diffusion Maps |
| diffuseMat | Generic diffusion function |
| diffuseMat2 | Generic diffusion function |
| diffuseProj | Predicts diffusion map projection from new data points |
| diffuse-SCD-method | Diffusion Maps |
| DiffusionMap-class | Diffusion Map dimensionality reduction on dataset |
| dim-SCD-method | Dimensions of SCD |
| doDE | Differential expression using Wilcoxon Ranks sum test |
| doDESeq | Differential expression using DESeq2 |
| eigenvals | Eigen values |
| eigenvals-DiffusionMap-method | Diffusion Map eigen values |
| eigenvals-reducedDim-method | Eigen values of Reduced Dimension object |
| eigenvecs | Eigen vectors |
| eigenvecs-DiffusionMap-method | Diffusion Map eigen vectors |
| eigenvecs-reducedDim-method | Eigen vectors |
| enrichr | Gene enrichment using Enrichr |
| estSizeFact | Estimates size factors as in DESeq. |
| estSizeFact2 | Estimate size factor supercharged |
| excludeCells | Exclude selected cells |
| excludeCells-SCD-method | Exclude selected cells |
| exportToMatlab | Writes data from single cell dataset object for use in Matlab |
| expressedGene | Identify expressed genes |
| exprs-SCD-method | Retrieve gene expression data from Single Cell Dataset object |
| facsPlot | Generate a FACS like plot from single-cell RNAseq data |
| fastDist | Fast vectorised Euclidean distance calculator |
| fData-SCD-method | Retrieve gene information table from Single Cell Dataset... |
| filterCell | Predicate indicating whether cell filtering is active |
| filterCell-SCD-method | Predicate indicating whether cell filtering is active. |
| filterCell-set | Set whether to use filter or not |
| filterCell-set-SCD-logical-method | Set cell filter. |
| filterGene | Predicate indicating whether gene filtering is active |
| filterGene-SCD-method | Predicate indicating whether gene filtering is active |
| filterGene-set | Set whether to use filter or not |
| filterGene-set-SCD-logical-method | Set gene filter. |
| filterQC | Predicate indicating whether filtering of cells that failed... |
| filterQC-SCD-method | Predicate indicating whether filtering of cells that failed... |
| filterQC-set | Set whether to use QC filter or not |
| filterQC-set-SCD-logical-method | Set QC filter. |
| findCells | Finds cells from SCD object matching query term |
| findGene | Find an approximate gene name |
| findLouvain | Louvain clustering on transition matrix |
| findPath | Find path between two selected cells |
| findPath-SCD-method | Find path between two selected cells |
| geneDistribution | Histogram of gene distribution |
| geneID2Name | Returns human readable gene names |
| geneName2id | Returns Ensembl id given a gene name |
| getDiffMap | Retrieves diffusion map object |
| getDiffMap-SCD-method | Retrieves diffusion map object |
| getIsomap | Retrieves Isomap object |
| getIsomap-SCD-method | Retrieves Isomap object |
| getMST | Retrieves the minimum spanning tree from the 'graph' slot of... |
| getMST-reducedDim-method | Retrieves the minimum spanning tree from the 'graph' slot of... |
| getMST-SCD-method | Retrieves the minimum spanning tree from the 'graph' slot of... |
| getMVP | Retrieve rendering data from current rgl plot |
| getPaths | Retrieve paths from a dimensionality reduced object |
| getPaths-reducedDim-method | Retrieve paths from a dimensionality reduced object |
| getPCA | Retrieves PCA object |
| getPCA-SCD-method | Retrieves PCA object |
| getTSNE | Retrieves t-SNE object |
| getTSNE-SCD-method | Retrieves t-SNE object |
| ggCol | Generate ggplot colors |
| heatmap.gottgens | Heatmap helper function for leaf re-ordering |
| heatmap.minus | Heatmap function based on heatmap.2 |
| initialize-SCD-method | To initialize a SCD object |
| Isomap-class | Isomap dimensionality reduced object |
| listEnrichrDbs | Look up available databases on Enrichr |
| loadings-PCA-method | PCA loadings |
| logVarGenes | Find highly variable genes (log linear model) |
| markFailedQC | Mark cells that have failed QC |
| markFailedQC-SCD-method | Mark cells that have failed QC |
| markGOI | Alters matrix rownames to only include genes of interest |
| memls | List variables ls() on steroids |
| mst | Minimum Spanning Tree for Reduced Dimensionality Object |
| mst-reducedDim-method | Minimum Spanning Tree for Reduced Dimensionality Object |
| mst-SCD-method | Generate minimum spanning true |
| multiGenes | Generates multiple 3D plots with marked gene expression |
| neatLabels | Decorate plots with log10 values |
| newSCD | Make a new SCD object |
| orderFrame | Reorder frame |
| PCA-class | Princincple Component Analysis on dataset |
| pData-SCD-method | Retrieve phenotype data |
| performQC | Perform QC on data |
| performQC-SCD-method | Perform QC on data |
| plot3 | 3D plotting function |
| plot3-reducedDim-method | 3D plotting function |
| plotGene | Visual representation of gene expression. |
| plotGeneProfile | Plots gene profile on trajectory |
| plotLegend | Plots legend for plotGene() function |
| plotPath3 | Plots path in 3D plot. Only to be called after 'plot3' |
| plotPath3-reducedDim-method | Plot path in 3D plot. Only to be called after 'plot3' |
| plotQC | Plots QC from SCD |
| plot-SCD-ANY-method | General plot function |
| plotTechVar | Plots a technical noise analysis plot |
| plotTree3 | Plots given path |
| prepData | Prepares data frame |
| printEnrich | Print Enrichr output to text file. |
| printGene | Produce pdf of 'plotGene' output |
| qc | Retrieve QC in counts |
| qcFunc | Quality control function |
| qc-SCD-method | Retrieve QC in counts |
| read.qPCR | Reads in qRT-PCR file |
| reducedDim-class | A virtual S4 class |
| removePath | Generic function to remove saved paths |
| removePath-reducedDim-method | Removes paths from object |
| removePath-SCD-method | Removes paths from object |
| resetCells | Include all cells |
| runPCA | Principal Component Analysis |
| runPCA-SCD-method | Principal Component Analysis |
| runTSNE | Perform t-distributed stochastic neighbour embedding |
| runTSNE-SCD-method | Perform t-distributed stochastic neighbour embedding |
| SCD-class | Single Cell Dataset |
| selectCells | Select cells function |
| selectCells-SCD-method | Select cells function |
| selectionTray | Selection Heatmap |
| selectVariableGenes | To select only highly variable genes for further analysis |
| selectVariableGenes-SCD-method | To select only highly variable genes for further analysis |
| sf | Retrieve size factors |
| sf-SCD-method | Retrieve size factors |
| sf-set | Save the size factors |
| sf-set-SCD-character-matrix-method | Save the size factors |
| slidingAv | Calculates sliding average |
| smoothGn | Gam smoothing of gene expression |
| sparseMarkov | Generate a sparse Markov matrix for momentum method to... |
| spikes | Retrieve spike in counts |
| spikes-SCD-method | Retrieve spike in counts |
| submap | Subset Heatmap. |
| techVar | Technical noise analysis for single cell RNAseq |
| techVar-SCD-method | Technical noise analysis for single cell RNAseq |
| techVarSub | Technical noise analysis for single cell RNAseq |
| TSNE-class | TSNE dimensionality reduction on dataset |
| useFilter | Add additional phenotype data |
| useFilter-SCD-method | Predicate indicating whether overall filtering is active |
| useFilter-set | Set whether to use filter or not |
| useFilter-set-SCD-logical-method | Set whether to use filter or not |
| winsor | Winsorization function |
| writeGeneList | Write a list of gene vectors to file |
