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

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