Man pages for Japrin/sscClust
simpler single cell RNAseq data clustering
| binarizeExp | binarize the expression value using the distribution |
| classifyCell.by.model | classify cells using pre-trained model |
| classifyCell.by.sigGene | classify cells using signature genes |
| classify.outlier | outlier detection using extremevalues |
| comb.pvalue | combine p values |
| expressedFraction | For each gene, calculate the frequency of cells in each... |
| expressedFraction.HiExpressorMean | For each gene, calculate the average expression of the... |
| fftRtsne | Wraper for running FIt-SNE. Code from KlugerLab... |
| findDEGenesByAOV | differential expression analysis |
| findKneePoint | Find the knee point of the scree plot |
| getAUC | calculate the AUC of one gene, using it as a classifier. code... |
| integrate.by.avg | integrate dataset by calculating the average expression and... |
| mcrf | Wraper for running random forest classifier (multiple core... |
| plotPairsCor | plot genes expression in pairs of clusters to examine the... |
| plotSigGene | plot signature genes |
| rank.de.gene | get gene ranking table from obj |
| reexports | Objects exported from other packages |
| run.DE.matrix | run DE given an expression matrix |
| run.KNN | Wraper for running random forest classifier |
| run.limma.matrix | run limma, given an expression matrix |
| run.RF | Wraper for running random forest classifier |
| run.SC3 | Wraper for running SC3 |
| run.SVM | Wraper for running svm |
| run.tSNE | Wraper for running Rtsne |
| sce.Pollen | Single cell RNA-Seq data extracted from a publication by... |
| ssc.clust | Perform clustering using reduced data |
| ssc.clusterMarkerGene | identify marker genes of each cluster |
| ssc.clustSubsamplingClassification | Clustering with subsampling and classification |
| ssc.DEGene.limma | identify differential genes of each cluster (comparing the... |
| ssc.reduceDim | Reduce dimension by various methods |
| ssc.run | Wrapper for running all the pipeline |
| ssc.variableGene | Identify variable genes |
