R: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

# A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

## Documentation for package ‘DIscBIO’ version 1.2.2

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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