DepMap-Analytics/CoRe
CoRe R package

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CoRe R package

.Rbuildignore
.gitignore
CoRe.Rproj
DESCRIPTION
NAMESPACE
R/CoRe.R README.md Reference_Manual.pdf
data/BAGEL_essential.RData
data/BAGEL_nonEssential.RData
data/EssGenes.DNA_REPLICATION_cons.RData
data/EssGenes.HISTONES.RData
data/EssGenes.KEGG_rna_polymerase.RData
data/EssGenes.PROTEASOME_cons.RData
data/EssGenes.SPLICEOSOME_cons.RData
data/EssGenes.ribosomalProteins.RData
data/curated_BAGEL_essential.RData
data/curated_BAGEL_nonEssential.RData
man/BAGEL_essential.Rd man/BAGEL_nonEssential.Rd man/CoRe.ADaM.Rd man/CoRe.AssembleFPs.Rd man/CoRe.Binarize_Matrix.Rd man/CoRe.CF_Benchmark.Rd man/CoRe.CS_ADaM.Rd man/CoRe.FiPer.Rd man/CoRe.PanCancer_ADaM.Rd man/CoRe.VisCFness.Rd man/CoRe.coreFitnessGenes.Rd man/CoRe.download_AnnotationModel.Rd man/CoRe.download_BinaryDepMatrix.Rd man/CoRe.download_DepMatrix.Rd man/CoRe.empiricalOdds.Rd man/CoRe.extract_tissueType_SubMatrix.Rd man/CoRe.generateNullModel.Rd man/CoRe.panessprofile.Rd man/CoRe.randomisedepMat.Rd man/CoRe.scale_to_essentials.Rd man/CoRe.tradeoffEO_TPR.Rd man/CoRe.truePositiveRate.Rd man/EssGenes.DNA_REPLICATION_cons.Rd man/EssGenes.HISTONES.Rd man/EssGenes.KEGG_rna_polymerase.Rd man/EssGenes.PROTEASOME_cons.Rd man/EssGenes.SPLICEOSOME_cons.Rd man/EssGenes.ribosomalProteins.Rd man/curated_BAGEL_essential.Rd man/curated_BAGEL_nonEssential.Rd
notebooks/.DS_Store
notebooks/.ipynb_checkpoints/CoRe_Benchmarking-checkpoint.ipynb
notebooks/CENtools/LR.py
notebooks/CENtools/__init__.py
notebooks/CENtools/clustering.R
notebooks/CENtools/curation.py
notebooks/CENtools/data/.DS_Store
notebooks/CENtools/data/curated_data/.DS_Store
notebooks/CENtools/data/curated_data/ADAM_Context_Genes.csv
notebooks/CENtools/data/curated_data/ADAM_Core_Fitness_Genes.csv
notebooks/CENtools/data/curated_data/Adam_Context_Score_df.csv
notebooks/CENtools/data/curated_data/Cores_for_pluoripotency_only.csv
notebooks/CENtools/data/curated_data/Curated_Bagel_Essential_Genes.txt
notebooks/CENtools/data/curated_data/Curated_Bagel_Non_Essential_Genes.txt
notebooks/CENtools/data/curated_data/Dede_etal_Core_genes.csv
notebooks/CENtools/data/curated_data/Kinase_TF_Surface_SLCs.txt
notebooks/CENtools/data/curated_data/Known_cores_for_all_Ihry_paper.csv
notebooks/CENtools/data/curated_data/STEM_Cores.csv
notebooks/CENtools/install.R
notebooks/CENtools/necessary_packages.py
notebooks/CENtools/objects.py
notebooks/CENtools/paths.py
notebooks/CENtools/requirements.txt
notebooks/Characterising_CFsets.R
notebooks/CoRe_Benchmarking.ipynb
notebooks/CoRe_Benchmarking_code_only_and_other_figures.R
notebooks/data/.DS_Store
notebooks/data/ADaM_CFs_Behan_et_Al_2019.RData
notebooks/data/BAGEL.py
notebooks/data/BAGEL_v2_Essentials.RData
notebooks/data/BF_matrix/Sanger_scaled_ADaM.RData
notebooks/data/BF_matrix/Sanger_scaled_Behan2019.RData
notebooks/data/BF_matrix/Sanger_scaled_CENtools.RData
notebooks/data/BF_matrix/Sanger_scaled_Hart2014.RData
notebooks/data/BF_matrix/Sanger_scaled_Hart2017.RData
notebooks/data/BF_matrix/Sanger_scaled_Sharma2020.RData
notebooks/data/BF_matrix/Sanger_scaled_curated_Hart2014.RData
notebooks/data/CEGv2.txt
notebooks/data/CFGs/ADaM.txt
notebooks/data/CFGs/Behan2019.txt
notebooks/data/CFGs/CENtools.txt
notebooks/data/CFGs/Hart2014.txt
notebooks/data/CFGs/Hart2017.txt
notebooks/data/CFGs/Sharma2020.txt
notebooks/data/CFGs/curated_Hart2014.txt
notebooks/data/CMP_RNAseq.Rdata
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notebooks/data/CRISPRcleaned_logFC/NMC-G1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/NUGC-3_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OACM5-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OAW-42_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OC-314_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OCI-AML2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OCI-AML3_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OCI-LY-19_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OCUB-M_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OE21_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OE33_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OPM-2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OSC-19_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OSC-20_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OV-90_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OVCA420_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OVCAR-3_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OVCAR-5_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OVCAR-8_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OVISE_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OVK-18_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/OVMIU_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PA-TU-8902_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PA-TU-8988T_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PANC-02-03_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PANC-03-27_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PANC-04-03_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PANC-08-13_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PANC-10-05_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PC-14_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PCI-15A_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PCI-30_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PCI-38_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PCI-4B_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PCI-6A_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PE-CA-PJ15_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PEO1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PEO4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PL4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/PSN1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RCC-FG2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RCM-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RERF-GC-1B_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RERF-LC-Sq1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RKN_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RKO_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RL95-2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RMG-I_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ROS-50_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/RPMI-8226_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SAS_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SCC-4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SCC-9_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SCC90_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SCH_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SF126_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SF295_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SF539_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SJSA-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-GT-4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-MEL-2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-MES-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-MG-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-N-AS_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-N-DZ_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-N-FI_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-N-SH_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SK-PN-DW_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SKN-3_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNB75_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNG-M_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNU-16_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNU-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNU-61_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNU-81_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNU-C1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SNU-C5_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SU-DHL-10_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SU-DHL-5_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SU-DHL-8_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SU8686_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SUIT-2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SW1088_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SW1573_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SW1990_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SW48_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SW620_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SW626_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/SW837_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/T-T_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/T47D_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/T84_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/T98G_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TC-71_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TE-10_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TE-4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TE-5_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TE-8_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TE-9_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TGW_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TMK-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TOV-112D_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TOV-21G_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/TYK-nu_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/U-87-MG_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/U251_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/UACC-893_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/UWB1.289_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/VMRC-LCD_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/YH-13_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/hTERT-RPE-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/no-10_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/no-11_corrected_logFCs.tsv.gz
notebooks/data/CenTools_essential_Sharma_et_al.txt
notebooks/data/Compendium_Cancer_Genes.tsv
notebooks/data/GTEx_Analysis_v6p_RNA-seq_RNA-SeQCv1.1.8_gene_median_rpkm.Rdata
notebooks/data/Kegg.DNArep.Rdata
notebooks/data/Kegg.Proteasome.Rdata
notebooks/data/Kegg.RNApoly.Rdata
notebooks/data/Kegg.Ribosome.Rdata
notebooks/data/Kegg.Spliceosome.Rdata
notebooks/data/PANCAN_simple_MOBEM.rdata
notebooks/data/col_13_distinct.RData
notebooks/data/col_57_distinct.RData
notebooks/data/common_genes.txt
notebooks/data/curated_NEG.txt
notebooks/data/dependency_with_biomarkers.txt
notebooks/data/early_ess.RData
notebooks/data/histones.RData
notebooks/data/late_ess.RData
notebooks/data/mid_ess.RData
notebooks/data/preComputed/ADaM.RData
notebooks/data/preComputed/CENtools.RData
notebooks/data/preComputed/CFs_sets.RData
notebooks/data/preComputed/CFs_sets_plus_training.RData
notebooks/data/preComputed/FiPer_outputs.RData
notebooks/data/preComputed/novelCFs_sets.RData
notebooks/data/protein-coding_genes_annot.txt
notebooks/data/run_bagel.sh
notebooks/data/screenedGenes.RData
notebooks/web/.DS_Store
notebooks/web/coRe_logo.jpg
notebooks/web/coRe_logo.pdf vignette/my-vignette.Rmd
vignette/rsconnect/documents/my-vignette.Rmd/rpubs.com/rpubs/Document.dcf
vignette/rsconnect/documents/my-vignette.Rmd/rpubs.com/rpubs/Publish Document.dcf
DepMap-Analytics/CoRe documentation built on July 6, 2022, 8:01 a.m.

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