Files in DepMap-Analytics/CoRe
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
notebooks/data/CRISPRcleaned_logFC/22RV1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/23132-87_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/42-MG-BA_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/769-P_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/8-MG-BA_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A172_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A2058_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A253_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A2780ADR_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A2780_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A2780cis_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A375_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/A549_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/AGS_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/AM-38_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ARH-77_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/AU565_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/AsPC-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/BB30-HNC_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/BE2-M17_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/BICR78_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/Becker_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/BxPC-3_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/C2BBe1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CAL-27_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CAL-33_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CAL-51_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CAL-72_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CAPAN-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CAS-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CHP-212_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/CL-11_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/COLO-205_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/COLO-320-HSR_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/COLO-678_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/COLO-680N_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/COLO-684_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/COLO-824_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/COR-L23_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/Ca9-22_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/Caov-4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/D-423MG_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/D-502MG_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/D-542MG_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/DAN-G_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/DBTRG-05MG_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/DK-MG_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/DOK_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/DOV13_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/DU-145_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/Detroit562_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/DiFi_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EBC-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EC-GI-10_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EFO-21_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EFO-27_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EGI-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EPLC-272H_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ES-2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ES4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ES5_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ES8_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ESO26_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ESO51_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/ESS-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EVSA-T_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/EW-16_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/FADU_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/GAMG_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/GB-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/GI-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/GP5d_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HARA_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC-15_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC-78_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC1143_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC1187_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC1395_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC1806_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC1937_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC1954_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC2998_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC38_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCC70_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCE-4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCT-116_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HCT-15_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HEC-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HGC-27_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HO-1-u-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HOP-62_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HPAF-II_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HSC-39_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/HT-29v1.0_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/HT55_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/Hs-578-T_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/Hs-683_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/HuP-T3_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/IGROV-1_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/IST-MEL1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/JHOS-2_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/JHOS-4_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/JHU-011_corrected_logFCs.tsv.gz
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notebooks/data/CRISPRcleaned_logFC/JHU-029_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/JIMT-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/KATOIII_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/KINGS-1_corrected_logFCs.tsv.gz
notebooks/data/CRISPRcleaned_logFC/KLE_corrected_logFCs.tsv.gz
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