Man pages for kendomaniac/rCASC
rCASC reproducible Classification Analysis of Single Cell Sequencing Data
| anovaLike | A function allowing the identification of differentially... |
| autocluster4clustering | Autoencoder clustering |
| autoencoder | Autoencoder |
| autoencoder4clustering | Autoencoder4clustering |
| autoencoder4clusteringGPU | Autoencoder4clustering |
| autoencoder4pseudoBulk | Autoencoder for pseudoBulk |
| autoencoderAnalysis | Autoencoder Analysis |
| autoencoderAnalysis4Clustering | Autoencoder Analysis |
| autoencoderClustering | Autoencoder clustering |
| autoencoderDB | Autoencoder4clustering |
| autoFeature | Feature selection for autoencoder |
| BCscTool | BCscTool |
| BCscWrapper | BCscTool_wrapper |
| 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 |
| clusteringWADB_Wrapper | wrapperAutoencoder |
| clusteringWA_Wrapper | wrapperAutoencoder |
| clusterNgriph | Defining with griph the range of number of clusters to be... |
| clusterReorg | Reorganize Cluster |
| clustersFeatures | A function to extract priority lists of genes from ANOVAlike... |
| clusterStability | Permutations and Clustering |
| 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... |
| deepClustering | deepClustering |
| deltaFilter | Filterin |
| demultiplexing | Generating running bcl2fastq |
| dePblkae | dePblkae |
| deTwoGroups | A function allowing the identification of differentially... |
| dimensions | Cells count table size |
| dockerTest | Testing if Docker is installed |
| downloadContainers | Download for the first time all containers embedded in the... |
| fastqc | A function to handle a docker containier executing fastqc |
| filterZeros | A function plotting the distribution of zeros in cells... |
| genesPrioritization | Gene prioritization with SIMLR |
| genesSelection | Genes selection from genesPrioritization output |
| genesUmi | Plotting genes to UMIs relationship. |
| geneVisualization | GeneVisualization |
| geneVisualization2 | GeneVisualization2 |
| geneVisualizationSpatial | GeneVisualization |
| 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... |
| integrationCircos | integrationCircos |
| integrationPblkae | integrationPblkae |
| integrationPsblk | integrationPsblk |
| logTransform | Shifted logarithm transformation |
| lorenzFilter | A function to handle sigle cell Lorenz Quality filter for... |
| 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... |
| scanpyBootstrap | Executing clustering with scanpy |
| scanpyPermutation | Scanpy Permutation |
| scAtomic | scAtomic |
| schcl | Assigning cell types |
| scnorm | Running SCnorm normalization |
| seuratBootstrap | Executing clustering with Seurat |
| seurat_ccycle | Seurat cell cycle |
| seuratIntegration | Seurat Integration |
| seuratIntegrationMulti | Seurat Integration |
| seuratIntegrationPermutation | Seurat Integration Permutation |
| seuratPCAEval | Estimating the range of PC components to be used in Seurat... |
| seuratPermutation | Seurat Permutation |
| seuratPrior | seuratprior |
| 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... |
| stpipeline | Spatial transcriptomics pipeline |
| subSetCell | Subset Cell |
| toprnk | toprnk |
| topx | A function to selectec top X on the basis of gene/transcript... |
| tsneBootstrap | Executing clustering with tSne |
| umap | umap |
| umiNorm | Running SCnorm normalization |
| unstableFiltering | unstableFiltering |
| vioHTMLByGenes | vioHTMLByGenes |
| wrapperAutoencoder | wrapperAutoencoder |
| wrapperClustersIntegration | integrationCircos |
| wrapperMixModelsUmap | wrapperMixModelsUmap |
