Predict Synthetic Lethality and Other Gene Dependency Relationships from Multiomics Data

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Documentation for package ‘MultiSEp’ version 4.1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

depMapCRISPRscores_subset	Example CRISPR score input matrix
depMapMUT_small	Example mutation data input matrix
depMapMUT_subset	Example mutation data input matrix
depMapTissue_subset	Example tissue data input matrix
depMapXPR_small	Example gene expression input matrix
depMapXPR_subset	Example gene expression input matrix
Formatted_MUTimpactMatrix	The output of 'mts_formatMatrix()' function for an example dataset.
mixModelClusters_depMapCRISPR	Clusters of samples (cell lines) from the 'mts_mixModelCluster' function for a small dataset of DepMap CRISPR scores.
mixModelClusters_depMapXPR	Clusters output from the 'mts_mixModelCluster' function for a toy DepMap expression dataset.
mixModelClusters_vignette	Clusters output from the 'mts_mixModelCluster' function for a DepMap expression data that is required for the vignette.
mRes	Example results for the 'mts_Mutation' function.
mts_clusterAvg	Determine average CRISPR score values for gene expression clusters
mts_Crispr	Investigate Gene Dependency Relationships with CRISPR and gene expression data
mts_crisprPartition	Partition CRISPR gene effect scores
mts_CrisprTS	Predict tissue-specific gene dependency relationships, evaluating differences in CRISPR scores for gene A between expression clusters for gene B (SynLeGG).
mts_formatMatrix	Format a matrix into a list of data frames that capture gene functional status
mts_GeneDepCrispr	CRISPR and gene expression gene-dependency prediction (SynLeGG)
mts_GeneDepID	CRISPR vs gene expression induced dependency pipeline (SynLeGG)
mts_GeneDepMutation	Mutation vs gene expression gene-dependency prediction
mts_genepairsChunkGeneration	Generate '.RData' files containing subsets of gene pairs
mts_InducedDependency	Predict 'induced dependency' relationships, evaluating differences in CRISPR scores for gene A between expression clusters for gene B
mts_mixModelCluster	Cluster continuous data with Gaussian Mixture Modelling
mts_mixModelCluster_XPR	Cluster gene expression data with Gaussian Mixture Modelling
mts_Mutation	Integrate gene cluster assignments with mutation data
mts_omics	Predict synthetic lethality and other dependency relationships from mutually exclusive loss of function patterns
mts_pairwiseExpressionPlot	Visualise pairwise gene expression data with MultiSEp cluster boundaries.
mts_patternDetection	Predict Gene Dependency Relationship Patterns, including Synthetic Lethality
mts_plotClusterDistribution	Visualise samples and pairwise gene expression clusters
mts_plotCRISPRGeneCluster	Visualise CRISPR and expression data (SynLeGG methods).
mts_plotMutation	Visualise clusters for one gene with the mutation status of another gene.
mts_targetCoverageFromMutations	Predict the therapeutic population coverage achieved by inhibition of a candidate target gene
mts_tests	Unit Tests for the MultiSEp package
multisepCrisprList	Example Multisep t-test CRISPR vs XPR results object.
multisepList	Example results from mts_clusterAvg()
MUT_impactMatrix	Example mutation impact matrix