├── Copyright.txt ├── Data ├── CRC_MSI.samples ├── CRC_POLE.samples ├── Different_FFPEloads │ ├── repaired_profiles_corrected_L1.csv │ ├── repaired_profiles_corrected_L2.csv │ ├── repaired_profiles_corrected_L3.csv │ ├── repaired_profiles_corrected_L4.csv │ ├── repaired_profiles_corrected_L5.csv │ ├── simulated_PCAWG_FFPE_repaired_L1.csv │ ├── simulated_PCAWG_FFPE_repaired_L2.csv │ ├── simulated_PCAWG_FFPE_repaired_L3.csv │ ├── simulated_PCAWG_FFPE_repaired_L4.csv │ ├── simulated_PCAWG_FFPE_repaired_L5.csv │ ├── simulated_PCAWG_FFPE_unrepaired_L1.csv │ ├── simulated_PCAWG_FFPE_unrepaired_L2.csv │ ├── simulated_PCAWG_FFPE_unrepaired_L3.csv │ ├── simulated_PCAWG_FFPE_unrepaired_L4.csv │ ├── simulated_PCAWG_FFPE_unrepaired_L5.csv │ ├── unrepaired_profiles_corrected_L1.csv │ ├── unrepaired_profiles_corrected_L2.csv │ ├── unrepaired_profiles_corrected_L3.csv │ ├── unrepaired_profiles_corrected_L4.csv │ └── unrepaired_profiles_corrected_L5.csv ├── FFPE_signatures_96-channel.csv ├── LocalFFPE_BeforeCorrection_profiles.csv ├── Refitting_Accuracy_80c_96c.csv ├── Refitting_Activities_Results_80c_96c.csv ├── SBS_signatures.csv ├── Selection_of_protocols_for_mainCancerTypes.csv ├── WGS_FFPEsamples.SBS96.csv ├── WGS_PCAWG.96.csv ├── WGS_PCAWG.activities.csv ├── WGS_opp.csv ├── fixiationgroup.txt ├── repaired_CRC_variant_simple.vcf ├── repaired_profiles_corrected.csv ├── simulated_PCAWG_FFPE_repaired.csv ├── simulated_PCAWG_FFPE_unrepaired.csv ├── study1_BaselineGroup_mutCounts.csv ├── study1_BlockageGroup_mutCounts.csv ├── study1_FixationGroup_mutCounts.csv ├── study1_gene_seq.fa ├── study2_FFPEonly_mutCounts.csv ├── study2_gene_seq.fa ├── study3_FFPE-only_mutations.vcf ├── study3_FFPE-only_mutations_count.csv ├── unrepaired_CRC_variant_simple.vcf ├── unrepaired_profiles_corrected.csv ├── well_corrected_repaired_FFPE.csv └── well_corrected_unrepaired_FFPE.csv ├── FFPEsig.py ├── FFPEsig_OUTPUT ├── ColoRect-AdenoCA::SP21528_after_correction.pdf ├── ColoRect-AdenoCA::SP21528_all_solutions.csv ├── ColoRect-AdenoCA::SP21528_before_correction.pdf └── ColoRect-AdenoCA::SP21528_corrected_profile.csv ├── Notebooks ├── Comparing_refitting_results_of_96c_80c_sig.ipynb ├── Correcting_FFPEnoise_in_WGS_FFPE_CRCs.ipynb ├── Correctting_FFPEnoise_in_SimulatedFFPEs_from_PCAWG.ipynb ├── FFPEsig_discovery.ipynb ├── SigDecomposition_using_corrected_and_uncorrected_FFPEprofiles_80c.ipynb └── simulation_code_for_reply1.8.ipynb ├── README.md ├── Source_Data.zip ├── docs ├── Comparing_refitting_results_of_96c_80c_sig.html ├── Correcting_FFPEnoise_in_WGS_FFPE_CRCs.html ├── Correctting_FFPEnoise_in_SimulatedFFPEs_from_PCAWG.html ├── FFPEsig_discovery.html ├── SigDecomposition_using_corrected_and_uncorrected_FFPEprofiles_80c.html ├── index.html └── simulation_code_for_reply1.8.html └── setup.py /Copyright.txt: -------------------------------------------------------------------------------- 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