Package index

Conda environment management

Modification interface

Set, update, remove conda environments

UpdateEnvCache(): Handy CondaEnvManger instance modifier

resetCache(): Reset a conda environment

saveToCache(): Save a conda environment manager to cache

Access interface

Show the current state of environments or the location of cache on disk

getCache(): Get current cache of conda environments

getCachePath(): Get path to package config cache

reloadCache(): Reload cache from disk

Class constructors

CondaEnv(): Handy CondaEnv instance constructor

CondaManager(): Handy CondaEnvManger instance constructor

Checkers

Check usability of conda environments

isValid(): Check the validity of conda environment's components

checkCondaBin() checkCondaEnvPath() checkCondaEnvName() checkCondaEnv(): Check the validity of conda environment's components

Data integration

Main interface

Integrate the layers of a Seurat object with one or more methods

DoIntegrate(): Integrate layers using one or multiple integration method(s)

Methods included in SeuratIntegrate

CombatIntegration(): Run ComBat on Seurat's Assay5 object through IntegrateLayers

HarmonyIntegration() HarmonyIntegration.fix(): Run Harmony on Seurat's Assay5 object through IntegrateLayers

MNNIntegration(): Run classical MNN on Seurat's Assay5 object through IntegrateLayers

ScanoramaIntegration(): Run Scanorama on Seurat's Assay5 object through IntegrateLayers

bbknnIntegration(): Run bbknn on Seurat's Assay5 object through IntegrateLayers

scANVIIntegration(): Run scANVI on Seurat's Assay5 object through IntegrateLayers

scVIIntegration() scVIIntegration.fix(): Run scVI on Seurat's Assay5 object through IntegrateLayers

trVAEIntegration(): Run trVAE on Seurat's Assay5 object through IntegrateLayers

Compatible methods from other packages

RPCAIntegration(): Seurat-RPCA Integration (from Seurat)

CCAIntegration(): Seurat-CCA Integration (from Seurat)

FastMNNIntegration(): Run fastMNN in Seurat 5 (from SeuratWrappers)

Scoring

Preprocessing

Useful functions to preprocess outputs before scoring

FindOptimalClusters(): Find a clustering that maximises NMI or ARI

CellCycleScoringPerBatch(): Score cell cycle phases per batch

Scoring

Functions to score integrations

ScoreARI() AddScoreARI(): Score a clustering result with adjusted rand index

ScoreASW() AddScoreASW() ScoreASWBatch() AddScoreASWBatch(): Score an embedding or a count matrix with the average silhouette width

ScoreRegressPC.CellCycle() AddScoreRegressPC.CellCycle(): Score a corrected or uncorrected PCA to estimate the contribution of S and G2M scores to variance

ScoreConnectivity() AddScoreConnectivity(): Score a knn graph based on cell-type label connectivity

ScoreDensityPC() AddScoreDensityPC(): Score a corrected or uncorrected PCA to estimate batch mixing

ScoreKBET() AddScoreKBET(): Score an embedding or a knn graph with the kBET test

AddScoreLISI() ScoreLISI(): Score a dimensionality reduction embedding or knn graph using the Local Inverse Simpson Index

ScoreNMI() AddScoreNMI(): Score a clustering result with normalised mutual information

ScoreRegressPC() AddScoreRegressPC(): Score a corrected or uncorrected PCA to estimate batch mixing

ScoreScGraph() AddScoreScGraph(): Score a dimension reduction by correlating normalised centroid distances

Postprocessing

Once AddScore[..] functions have been run, scores are to be scaled then plotted

ScaleScores(): Scale the scores in the score tibble to plot them

PlotScores(): Visualise and compare the performances of integration algorithms

General getters and setters of score table

Get, set, modify scores in a more flexible way

GetMiscIntegrations() GetMiscScores() IntegrationScores(): Retrieve integration scores from a Seurat object

SetMiscScore(): Set the value of a score in the score tibble

AddMiscIntegrations() AddMiscScores(): Add integration(s) or score(s) slot(s) to the score tibble

Graph-based utilities

Graph manipulation

Handy functions to manipulate and modify graphs

SymmetrizeKnn(): Symmetrize a nearest neighbours graph

CutKnn(): Remove excessive number of neighbours in a knn graph

ExpandNeighbours(): Expand knn graph to increase the number of neighbours

GetConnectivities(): Derive connectivities from distances

Connectivity between batches

Handy functions to overview inter- and intra-batches connections in a knn graph

GetPropInterBatch(): Calculate proportion of nearest neighbours between batches

GetPropIntraBatch(): Calculate proportion of nearest neighbours within batches

Utility functions for matrices

Functions designed for smaller-scale, auxiliary tasks on matrices.

Matrix normalisation

NormaliseL2(): Normalise a matrix using L2 norm

Conda environment management

Modification interface

Access interface

Class constructors

Checkers

Data integration

Main interface

Methods included in SeuratIntegrate

Compatible methods from other packages

Scoring

Preprocessing

Scoring

Postprocessing

General getters and setters of score table

Graph-based utilities

Graph manipulation

Connectivity between batches

Utility functions for matrices

Matrix normalisation

Matrix sorting

Sparse matrix symmetry

Matrix sorting

Conversion of matrix indices