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 |
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