All functions

anovaLike()

A function allowing the identification of differentially expressed genes.

autoFeature()

Feature selection for autoencoder

autoencoder()

Autoencoder

autoencoderAnalysis()

Autoencoder Analysis

autoencoderClustering()

Autoencoder clustering

bootstrapsVideo()

Bootstraps vide

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

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.

deTwoGroups()

A function allowing the identification of differentially expressed genes.

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

genesPrioritization()

Gene prioritization with SIMLR

genesSelection()

Genes selection from genesPrioritization output

genesUmi()

Plotting genes to UMIs relationship.

griphBootstrap()

Executing clustering with griph.

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

lorenzFilter()

A function to handle sigle cell Lorenz Quality filter for Single-cells

mergeMatrix()

Merge matrix

mitoRiboUmi()

MitoRiboUmi

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

scannobyGtf()

Annotating single cell counts table using ENSEMBL gtf and refGenome CRAN package

scanpyBootstrap()

Executing clustering with scanpy

scanpyPermutation()

Scanpy Permutation

scnorm()

Running SCnorm normalization

seuratBootstrap()

Executing clustering with Seurat

seuratPCAEval()

Estimating the range of PC components to be used in Seurat clustering

seuratPermutation()

Seurat Permutation

seuratPrior()

seuratprior

sharpBootstrap()

Executing clustering with SHARP.

simlrBootstrap()

Clustering with SIMLR

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

topx()

A function to selectec top X on the basis of gene/transcript expression

tsneBootstrap()

Executing clustering with tSne

umiNorm()

Running SCnorm normalization

unstableFiltering()

unstableFiltering

wrapperAutoencoder()

wrapperAutoencoder