Man pages for DepMap-Analytics/CoRe
CoRe R package
| BAGEL_essential | Reference Core fitness essential genes |
| BAGEL_nonEssential | Reference set of non essential genes |
| CoRe.ADaM | Adaptive Daisy Model to compute core fitness genes |
| CoRe.AssembleFPs | Assembling expression-based false positives |
| CoRe.Binarize_Matrix | Binarize Quantitative Dependency Matrix |
| CoRe.CF_Benchmark | Recall of known essential genes and ROC indicators |
| CoRe.coreFitnessGenes | Determining Core Fitness from a binary dependency matrix and... |
| CoRe.CS_ADaM | Execute ADaM on a specific tissue/cancer type |
| CoRe.download_AnnotationModel | Download Cell Passport models annotation file |
| CoRe.download_BinaryDepMatrix | Download Binary Dependency Matrix |
| CoRe.download_DepMatrix | Download Quantitative Dependency Matrix |
| CoRe.empiricalOdds | Empirical odds of number of fitness genes per number of cell... |
| CoRe.extract_tissueType_SubMatrix | Subset Dependency Matrix based on tissue/cancer type of... |
| CoRe.FiPer | Fitness Percentile method to estimate common essential genes |
| CoRe.generateNullModel | Null model of number of fitness genes across numbers of cell... |
| CoRe.PanCancer_ADaM | Execute ADaM at the Pan-cancer level |
| CoRe.panessprofile | Profile of number of fitness genes across fixed numbers of... |
| CoRe.randomisedepMat | Column-wise matrix randomisation |
| CoRe.scale_to_essentials | Scale matrix cell-wise using positive and negative reference... |
| CoRe.tradeoffEO_TPR | Calculate ADaM threshold |
| CoRe.truePositiveRate | Profile of True Positive Rates |
| CoRe.VisCFness | Common-essentiality tendency visualisation |
| curated_BAGEL_essential | Curated Reference Core fitness essential genes |
| curated_BAGEL_nonEssential | Curated Reference Core fitness essential genes |
| EssGenes.DNA_REPLICATION_cons | Core Fitness essential genes involved in DNA replication |
| EssGenes.HISTONES | Core Fitness essential histone genes |
| EssGenes.KEGG_rna_polymerase | Core Fitness essential rna polymerase genes |
| EssGenes.PROTEASOME_cons | Core Fitness essential proteasome genes |
| EssGenes.ribosomalProteins | Core Fitness essential genes coding for ribosomal proteins |
| EssGenes.SPLICEOSOME_cons | Core Fitness essential spliceosome genes |
