Man pages for kendomaniac/rCASC
rCASC reproducible Classification Analysis of Single Cell Sequencing Data

anovaLikeA function allowing the identification of differentially...
autocluster4clusteringAutoencoder clustering
autoencoderAutoencoder
autoencoder4clusteringAutoencoder4clustering
autoencoder4clusteringGPUAutoencoder4clustering
autoencoder4pseudoBulkAutoencoder for pseudoBulk
autoencoderAnalysisAutoencoder Analysis
autoencoderAnalysis4ClusteringAutoencoder Analysis
autoencoderClusteringAutoencoder clustering
autoencoderDBAutoencoder4clustering
autoFeatureFeature selection for autoencoder
BCscToolBCscTool
BCscWrapperBCscTool_wrapper
bootstrapsVideoBootstraps vide
bulkClustersbulkClusters
ccRemoveCc remove
cellCycle2Cell Cycle
cellrangerCountCellranger count
cellrangerIndexingCellranger indexing
checkCountDepthRunning SCnorm checkCountDepth test.
clusterIdentificationCluster identification
clusteringWADB_WrapperwrapperAutoencoder
clusteringWA_WrapperwrapperAutoencoder
clusterNgriphDefining with griph the range of number of clusters to be...
clusterReorgReorganize Cluster
clustersFeaturesA function to extract priority lists of genes from ANOVAlike...
clusterStabilityPermutations and Clustering
cometscMarker genes discovery with COMETSC
cometsc2Marker genes discovery with COMETSC for autoencoder results
counts2logA function to convert raw count in log counts
crossLabelCross Label
csvToSparsecsv to Sparse
deDetectionA function allowing the identification of differentially...
deepClusteringdeepClustering
deltaFilterFilterin
demultiplexingGenerating running bcl2fastq
dePblkaedePblkae
deTwoGroupsA function allowing the identification of differentially...
dimensionsCells count table size
dockerTestTesting if Docker is installed
downloadContainersDownload for the first time all containers embedded in the...
fastqcA function to handle a docker containier executing fastqc
filterZerosA function plotting the distribution of zeros in cells...
genesPrioritizationGene prioritization with SIMLR
genesSelectionGenes selection from genesPrioritization output
genesUmiPlotting genes to UMIs relationship.
geneVisualizationGeneVisualization
geneVisualization2GeneVisualization2
geneVisualizationSpatialGeneVisualization
gibbsRgibbsR
griphBootstrapExecuting clustering with griph.
gseaXLmHGgseaXLmHG
h5tocsvsparse to dense
harmonyHarmony
hfchfc, heatmap for clustering
houseKeephouseKeep Filtering
imputeImputing dropouts
indropCountsA function to handle a indrop V2 single cell data
indropIndexA function to create a genome index for indrop V2 single cell...
integrationCircosintegrationCircos
integrationPblkaeintegrationPblkae
integrationPsblkintegrationPsblk
logTransformShifted logarithm transformation
lorenzFilterA function to handle sigle cell Lorenz Quality filter for...
mergeMatrixMerge matrix
mitoRiboUmiMitoRiboUmi
mixcrmixcr
mixmodelsmixModels
nClusterEvaluationSIMLREvaluation of the numbur of optimal clusters
permAnalysisPermutation Analysis
permAnalysisGriphPermutation Analysis Griph
permAnalysisSeuratPermutation Analysis Seurat
permutationClusteringPermutations and Clustering
permutationClusteringSHARPPermutations and Clustering
permutationMoviePermutation Movie
recatPredictionCell Cycle
runDockerRun docker container
saverSaver
scannobyGtfAnnotating single cell counts table using ENSEMBL gtf and...
scanpyBootstrapExecuting clustering with scanpy
scanpyPermutationScanpy Permutation
schclAssigning cell types
scnormRunning SCnorm normalization
seuratBootstrapExecuting clustering with Seurat
seurat_ccycleSeurat cell cycle
seuratIntegrationSeurat Integration
seuratIntegrationMultiSeurat Integration
seuratIntegrationPermutationSeurat Integration Permutation
seuratPCAEvalEstimating the range of PC components to be used in Seurat...
seuratPermutationSeurat Permutation
seuratPriorseuratprior
sharpBootstrapExecuting clustering with SHARP.
simlrBootstrapClustering with SIMLR
slogosRslogosR
spatialAnalysisspatial Analysis
spatialAnalysis2spatial Analysis Plus
splitClustersSplit Matrix for each clusters
sraDownloadA function to handle fasterq-dumper SRA to download SRA fastq...
stpipelineSpatial transcriptomics pipeline
subSetCellSubset Cell
toprnktoprnk
topxA function to selectec top X on the basis of gene/transcript...
tsneBootstrapExecuting clustering with tSne
umapumap
umiNormRunning SCnorm normalization
unstableFilteringunstableFiltering
vioHTMLByGenesvioHTMLByGenes
wrapperAutoencoderwrapperAutoencoder
wrapperClustersIntegrationintegrationCircos
wrapperMixModelsUmapwrapperMixModelsUmap
kendomaniac/rCASC documentation built on May 18, 2024, 1:01 a.m.