Function reference • rCASC

All functions
`BCscTool()`	BCscTool
`BCscWrapper()`	BCscTool_wrapper
`anovaLike()`	A function allowing the identification of differentially expressed genes.
`autoFeature()`	Feature selection for autoencoder
`autocluster4clustering()`	Autoencoder clustering
`autoencoder()`	Autoencoder
`autoencoder4clustering()`	Autoencoder4clustering
`autoencoder4clusteringGPU()`	Autoencoder4clustering
`autoencoder4pseudoBulk()`	Autoencoder for pseudoBulk
`autoencoderAnalysis()`	Autoencoder Analysis
`autoencoderAnalysis4Clustering()`	Autoencoder Analysis
`autoencoderClustering()`	Autoencoder clustering
`autoencoderDB()`	Autoencoder4clustering
`bootstrapsVideo()`	Bootstraps vide
`bulkClusters()`	bulkClusters
`ccRemove()`	Cc remove
`cellCycle2()`	Cell Cycle
`cellrangerCount()`	Cellranger count
`cellrangerIndexing()`	Cellranger indexing
`checkCountDepth()`	Running SCnorm checkCountDepth test.
`clusterIdentification()`	Cluster identification
`clusterNgriph()`	Defining with griph the range of number of clusters to be used with SIMLR
`clusterReorg()`	Reorganize Cluster
`clusterStability()`	Permutations and Clustering
`clusteringWADB_Wrapper()`	wrapperAutoencoder
`clusteringWA_Wrapper()`	wrapperAutoencoder
`clustersFeatures()`	A function to extract priority lists of genes from ANOVAlike output
`cometsc()`	Marker genes discovery with COMETSC
`cometsc2()`	Marker genes discovery with COMETSC for autoencoder results
`counts2log()`	A function to convert raw count in log counts
`crossLabel()`	Cross Label
`csvToSparse()`	csv to Sparse
`deDetection()`	A function allowing the identification of differentially expressed genes.
`dePblkae()`	dePblkae
`deTwoGroups()`	A function allowing the identification of differentially expressed genes.
`deepClustering()`	deepClustering
`deltaFilter()`	Filterin
`demultiplexing()`	Generating running bcl2fastq
`dimensions()`	Cells count table size
`dockerTest()`	Testing if Docker is installed
`downloadContainers()`	Download for the first time all containers embedded in the workflows
`fastqc()`	A function to handle a docker containier executing fastqc
`filterZeros()`	A function plotting the distribution of zeros in cells eliminating all genes without a certain fraction of 0 in the samples
`geneVisualization()`	GeneVisualization
`geneVisualization2()`	GeneVisualization2
`geneVisualizationSpatial()`	GeneVisualization
`genesPrioritization()`	Gene prioritization with SIMLR
`genesSelection()`	Genes selection from genesPrioritization output
`genesUmi()`	Plotting genes to UMIs relationship.
`gibbsR()`	gibbsR
`griphBootstrap()`	Executing clustering with griph.
`gseaXLmHG()`	gseaXLmHG
`h5tocsv()`	sparse to dense
`harmony()`	Harmony
`hfc()`	hfc, heatmap for clustering
`houseKeep()`	houseKeep Filtering
`impute()`	Imputing dropouts
`indropCounts()`	A function to handle a indrop V2 single cell data
`indropIndex()`	A function to create a genome index for indrop V2 single cell data
`integrationCircos()`	integrationCircos
`integrationPblkae()`	integrationPblkae
`integrationPsblk()`	integrationPsblk
`logTransform()`	Shifted logarithm transformation
`lorenzFilter()`	A function to handle sigle cell Lorenz Quality filter for Single-cells
`mergeMatrix()`	Merge matrix
`mitoRiboUmi()`	MitoRiboUmi
`mixcr()`	mixcr
`mixmodels()`	mixModels
`nClusterEvaluationSIMLR()`	Evaluation of the numbur of optimal clusters
`permAnalysis()`	Permutation Analysis
`permAnalysisGriph()`	Permutation Analysis Griph
`permAnalysisSeurat()`	Permutation Analysis Seurat
`permutationClustering()`	Permutations and Clustering
`permutationClusteringSHARP()`	Permutations and Clustering
`permutationMovie()`	Permutation Movie
`recatPrediction()`	Cell Cycle
`runDocker()`	Run docker container
`saver()`	Saver
`scannobyGtf()`	Annotating single cell counts table using ENSEMBL gtf and refGenome CRAN package
`scanpyBootstrap()`	Executing clustering with scanpy
`scanpyPermutation()`	Scanpy Permutation
`schcl()`	Assigning cell types
`scnorm()`	Running SCnorm normalization
`seuratBootstrap()`	Executing clustering with Seurat
`seuratIntegration()`	Seurat Integration
`seuratIntegrationMulti()`	Seurat Integration
`seuratIntegrationPermutation()`	Seurat Integration Permutation
`seuratPCAEval()`	Estimating the range of PC components to be used in Seurat clustering
`seuratPermutation()`	Seurat Permutation
`seuratPrior()`	seuratprior
`seurat_ccycle()`	Seurat cell cycle
`sharpBootstrap()`	Executing clustering with SHARP.
`simlrBootstrap()`	Clustering with SIMLR
`slogosR()`	slogosR
`spatialAnalysis()`	spatial Analysis
`spatialAnalysis2()`	spatial Analysis Plus
`splitClusters()`	Split Matrix for each clusters
`sraDownload()`	A function to handle fasterq-dumper SRA to download SRA fastq files
`stpipeline()`	Spatial transcriptomics pipeline
`subSetCell()`	Subset Cell
`toprnk()`	toprnk
`topx()`	A function to selectec top X on the basis of gene/transcript expression
`tsneBootstrap()`	Executing clustering with tSne
`umap()`	umap
`umiNorm()`	Running SCnorm normalization
`unstableFiltering()`	unstableFiltering
`vioHTMLByGenes()`	vioHTMLByGenes
`wrapperAutoencoder()`	wrapperAutoencoder
`wrapperClustersIntegration()`	integrationCircos
`wrapperMixModelsUmap()`	wrapperMixModelsUmap

Reference

All functions