annotate_simulated_variants | Annotating base substitutions generated by... |
cosine | Similarity function for signatures |
gen_chrom | Chromosome generic |
gen_chrom-GeneFeatures-method | Chromosome method for GeneFeatures class |
gen_chrom-set | Assignable chromosome generic |
gen_chrom-set-GeneFeatures-character-method | Chromosome replacement method for GeneFeatures class |
GeneFeatures-class | An S4 class to represent a set of features of a gene. |
generate_mutations | Generating base substitutions based on silent mutation rate |
get_all_features | Get the required features for each gene |
get_all_probabilities | Calculate mutation probability distribution per gene |
get_chromosomes | Matching TxDb gene names with their chromosomes |
min_ranges | Simplifying GRanges |
MutSim | MutSim: A package for generating cancer mutations in genes... |
name | Name generic |
name-GeneFeatures-method | Name method for GeneFeatures class |
name-set | Assignable name generic |
name-set-GeneFeatures-character-method | Name replacement method for GeneFeatures class |
positions | Positions generic |
positions-GeneFeatures-method | Positions method for GeneFeatures class |
positions-set | Assignable positions generic |
positions-set-GeneFeatures-numeric-method | Positions replacement method for GeneFeatures class |
RevCom | Simple reverse complement for trinuleotides |
RevComMutType | Simple reverse complement for mutation types |
tri.counts | tri.counts generic |
tri.counts-GeneFeatures-method | tri.counts method for GeneFeatures class |
tri.counts-set | Assignable tri.counts generic |
tri.counts-set-GeneFeatures-numeric-method | tri.counts replacement method for GeneFeatures class |
trinucleotides | Trinucleotides generic |
trinucleotides-GeneFeatures-method | Trinucleotides method for GeneFeatures class |
trinucleotides-set | Assignable trinucleotides generic |
trinucleotides-set-GeneFeatures-character-method | Trinucleotides replacement method for GeneFeatures class |
upload_signatures | Upload cancer signatures and mutation types from COSMIC |
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