as.DISCBIO |
Convert Single Cell Data Objects to DISCBIO. |
check.format |
Check format |
ClassVectoringDT |
Generating a class vector to be used for the decision tree analysis. |
ClassVectoringDT-method |
Generating a class vector to be used for the decision tree analysis. |
ClustDiffGenes |
ClustDiffGenes |
ClustDiffGenes-method |
ClustDiffGenes |
Clustexp |
Clustering of single-cell transcriptome data |
Clustexp-method |
Clustering of single-cell transcriptome data |
clustheatmap |
Plotting clusters in a heatmap representation of the cell distances |
clustheatmap-method |
Plotting clusters in a heatmap representation of the cell distances |
comptSNE |
Computing tSNE |
comptSNE-method |
Computing tSNE |
customConvertFeats |
Automatic Feature Id Conversion. |
DEGanalysis |
Determining differentially expressed genes (DEGs) between all individual clusters. |
DEGanalysis-method |
Determining differentially expressed genes (DEGs) between all individual clusters. |
DEGanalysis2clust |
Determining differentially expressed genes (DEGs) between two particular clusters. |
DEGanalysis2clust-method |
Determining differentially expressed genes (DEGs) between two particular clusters. |
DISCBIO |
The DISCBIO Class |
DISCBIO-class |
The DISCBIO Class |
DISCBIO-class, |
The DISCBIO Class |
DISCBIO2SingleCellExperiment |
Convert a DISCBIO object to a SingleCellExperiment. |
Exprmclust |
Performing Model-based clustering on expression values |
Exprmclust-method |
Performing Model-based clustering on expression values |
FinalPreprocessing |
Final Preprocessing |
FinalPreprocessing-method |
Final Preprocessing |
FindOutliers |
Inference of outlier cells |
FindOutliers-method |
Inference of outlier cells |
foldchange.seq.twoclass.unpaired |
Foldchange of twoclass unpaired sequencing data |
HumanMouseGeneIds |
Human and Mouse Gene Identifiers. |
J48DT |
J48 Decision Tree |
J48DTeval |
Evaluating the performance of the J48 decision tree. |
Jaccard |
Jaccard’s similarity |
KmeanOrder |
Pseudo-time ordering based on k-means clusters |
KmeanOrder-method |
Pseudo-time ordering based on k-means clusters |
NetAnalysis |
Networking analysis. |
Networking |
Plotting the network. |
NoiseFiltering |
Noise Filtering |
NoiseFiltering-method |
Noise Filtering |
Normalizedata |
Normalizing and filtering |
Normalizedata-method |
Normalizing and filtering |
PCAplotSymbols |
Plot PCA symbols |
PCAplotSymbols-method |
Plot PCA symbols |
plotExptSNE |
Highlighting gene expression in the t-SNE map |
plotExptSNE-method |
Highlighting gene expression in the t-SNE map |
plotGap |
Plotting Gap Statistics |
plotGap-method |
Plotting Gap Statistics |
plotLabelstSNE |
tSNE map with labels |
plotLabelstSNE-method |
tSNE map with labels |
PlotMBpca |
Plotting pseudo-time ordering or gene expression in Model-based clustering in PCA |
PlotmclustMB |
Plotting the Model-based clusters in PCA. |
PlotmclustMB-method |
Plotting the Model-based clusters in PCA. |
plotOrderTsne |
Plotting the pseudo-time ordering in the t-SNE map |
plotOrderTsne-method |
Plotting the pseudo-time ordering in the t-SNE map |
plotSilhouette |
Silhouette Plot for K-means clustering |
plotSilhouette-method |
Silhouette Plot for K-means clustering |
plotSymbolstSNE |
tSNE map for K-means clustering with symbols |
plotSymbolstSNE-method |
tSNE map for K-means clustering with symbols |
plottSNE |
tSNE map |
plottSNE-method |
tSNE map |
PPI |
Defining protein-protein interactions (PPI) over a list of genes, |
prepExampleDataset |
Prepare Example Dataset |
pseudoTimeOrdering |
Pseudo-time ordering |
pseudoTimeOrdering-method |
Pseudo-time ordering |
rankcols |
Rank columns |
reformatSiggenes |
Reformat Siggenes Table |
replaceDecimals |
Replace Decimals |
resa |
Resampling |
retrieveURL |
Retries a URL |
RpartDT |
RPART Decision Tree |
RpartEVAL |
Evaluating the performance of the RPART Decision Tree. |
sammy |
Significance analysis of microarrays |
samr.estimate.depth |
Estimate sequencing depths |
valuesG1msTest |
Single-cells data from a myxoid liposarcoma cell line |
VolcanoPlot |
Volcano Plot |
wilcoxon.unpaired.seq.func |
Twoclass Wilcoxon statistics |