Man pages for wjawaid/bglab
Berthold Gottgens lab scRNA seq

addPathStore path
addPath-reducedDim-methodStore path
addPath-SCD-methodStore path
addPhenoAdd additional phenotype data
addPheno-SCD-methodAdd additional phenotype data
applyGaussianKernelwithVariableSigmaApply Gaussian Kernel using Laleh Haghverdi's variable sigma
applyMVPApplies transformation from rgl plot to data
bglabGottgens Lab Toolkit
clipboardCopy R content to clipboard
clustLouvainPerform Louvain clustering
colorGradientHelper function for 'plotGene'
counts-SCD-methodRetrieve counts data from Single Cell Dataset object
diffuseDiffusion Maps
diffuseMatGeneric diffusion function
diffuseMat2Generic diffusion function
diffuseProjPredicts diffusion map projection from new data points
diffuse-SCD-methodDiffusion Maps
DiffusionMap-classDiffusion Map dimensionality reduction on dataset
dim-SCD-methodDimensions of SCD
doDEDifferential expression using Wilcoxon Ranks sum test
doDESeqDifferential expression using DESeq2
eigenvalsEigen values
eigenvals-DiffusionMap-methodDiffusion Map eigen values
eigenvals-reducedDim-methodEigen values of Reduced Dimension object
eigenvecsEigen vectors
eigenvecs-DiffusionMap-methodDiffusion Map eigen vectors
eigenvecs-reducedDim-methodEigen vectors
enrichrGene enrichment using Enrichr
estSizeFactEstimates size factors as in DESeq.
estSizeFact2Estimate size factor supercharged
excludeCellsExclude selected cells
excludeCells-SCD-methodExclude selected cells
exportToMatlabWrites data from single cell dataset object for use in Matlab
expressedGeneIdentify expressed genes
exprs-SCD-methodRetrieve gene expression data from Single Cell Dataset object
facsPlotGenerate a FACS like plot from single-cell RNAseq data
fastDistFast vectorised Euclidean distance calculator
fData-SCD-methodRetrieve gene information table from Single Cell Dataset...
filterCellPredicate indicating whether cell filtering is active
filterCell-SCD-methodPredicate indicating whether cell filtering is active.
filterCell-setSet whether to use filter or not
filterCell-set-SCD-logical-methodSet cell filter.
filterGenePredicate indicating whether gene filtering is active
filterGene-SCD-methodPredicate indicating whether gene filtering is active
filterGene-setSet whether to use filter or not
filterGene-set-SCD-logical-methodSet gene filter.
filterQCPredicate indicating whether filtering of cells that failed...
filterQC-SCD-methodPredicate indicating whether filtering of cells that failed...
filterQC-setSet whether to use QC filter or not
filterQC-set-SCD-logical-methodSet QC filter.
findCellsFinds cells from SCD object matching query term
findGeneFind an approximate gene name
findLouvainLouvain clustering on transition matrix
findPathFind path between two selected cells
findPath-SCD-methodFind path between two selected cells
geneDistributionHistogram of gene distribution
geneID2NameReturns human readable gene names
geneName2idReturns Ensembl id given a gene name
getDiffMapRetrieves diffusion map object
getDiffMap-SCD-methodRetrieves diffusion map object
getIsomapRetrieves Isomap object
getIsomap-SCD-methodRetrieves Isomap object
getMSTRetrieves the minimum spanning tree from the 'graph' slot of...
getMST-reducedDim-methodRetrieves the minimum spanning tree from the 'graph' slot of...
getMST-SCD-methodRetrieves the minimum spanning tree from the 'graph' slot of...
getMVPRetrieve rendering data from current rgl plot
getPathsRetrieve paths from a dimensionality reduced object
getPaths-reducedDim-methodRetrieve paths from a dimensionality reduced object
getPCARetrieves PCA object
getPCA-SCD-methodRetrieves PCA object
getTSNERetrieves t-SNE object
getTSNE-SCD-methodRetrieves t-SNE object
ggColGenerate ggplot colors
heatmap.gottgensHeatmap helper function for leaf re-ordering
heatmap.minusHeatmap function based on heatmap.2
initialize-SCD-methodTo initialize a SCD object
Isomap-classIsomap dimensionality reduced object
listEnrichrDbsLook up available databases on Enrichr
loadings-PCA-methodPCA loadings
logVarGenesFind highly variable genes (log linear model)
markFailedQCMark cells that have failed QC
markFailedQC-SCD-methodMark cells that have failed QC
markGOIAlters matrix rownames to only include genes of interest
memlsList variables ls() on steroids
mstMinimum Spanning Tree for Reduced Dimensionality Object
mst-reducedDim-methodMinimum Spanning Tree for Reduced Dimensionality Object
mst-SCD-methodGenerate minimum spanning true
multiGenesGenerates multiple 3D plots with marked gene expression
neatLabelsDecorate plots with log10 values
newSCDMake a new SCD object
orderFrameReorder frame
PCA-classPrincincple Component Analysis on dataset
pData-SCD-methodRetrieve phenotype data
performQCPerform QC on data
performQC-SCD-methodPerform QC on data
plot33D plotting function
plot3-reducedDim-method3D plotting function
plotGeneVisual representation of gene expression.
plotGeneProfilePlots gene profile on trajectory
plotLegendPlots legend for plotGene() function
plotPath3Plots path in 3D plot. Only to be called after 'plot3'
plotPath3-reducedDim-methodPlot path in 3D plot. Only to be called after 'plot3'
plotQCPlots QC from SCD
plot-SCD-ANY-methodGeneral plot function
plotTechVarPlots a technical noise analysis plot
plotTree3Plots given path
prepDataPrepares data frame
printEnrichPrint Enrichr output to text file.
printGeneProduce pdf of 'plotGene' output
qcRetrieve QC in counts
qcFuncQuality control function
qc-SCD-methodRetrieve QC in counts
read.qPCRReads in qRT-PCR file
reducedDim-classA virtual S4 class
removePathGeneric function to remove saved paths
removePath-reducedDim-methodRemoves paths from object
removePath-SCD-methodRemoves paths from object
resetCellsInclude all cells
runPCAPrincipal Component Analysis
runPCA-SCD-methodPrincipal Component Analysis
runTSNEPerform t-distributed stochastic neighbour embedding
runTSNE-SCD-methodPerform t-distributed stochastic neighbour embedding
SCD-classSingle Cell Dataset
selectCellsSelect cells function
selectCells-SCD-methodSelect cells function
selectionTraySelection Heatmap
selectVariableGenesTo select only highly variable genes for further analysis
selectVariableGenes-SCD-methodTo select only highly variable genes for further analysis
sfRetrieve size factors
sf-SCD-methodRetrieve size factors
sf-setSave the size factors
sf-set-SCD-character-matrix-methodSave the size factors
slidingAvCalculates sliding average
smoothGnGam smoothing of gene expression
sparseMarkovGenerate a sparse Markov matrix for momentum method to...
spikesRetrieve spike in counts
spikes-SCD-methodRetrieve spike in counts
submapSubset Heatmap.
techVarTechnical noise analysis for single cell RNAseq
techVar-SCD-methodTechnical noise analysis for single cell RNAseq
techVarSubTechnical noise analysis for single cell RNAseq
TSNE-classTSNE dimensionality reduction on dataset
useFilterAdd additional phenotype data
useFilter-SCD-methodPredicate indicating whether overall filtering is active
useFilter-setSet whether to use filter or not
useFilter-set-SCD-logical-methodSet whether to use filter or not
winsorWinsorization function
writeGeneListWrite a list of gene vectors to file
wjawaid/bglab documentation built on May 4, 2019, 6:33 a.m.