Files in drake69/semseeker

Stochastic Epigenetic Mutations SEM Seeker

..Rcheck/semseeker-manual.pdf ..Rcheck/tests/tastthat.R ..Rcheck/tests/testthat/test-analyzePopulation.R ..Rcheck/tests/testthat/test-analyzeSingleSample.R ..Rcheck/tests/testthat/test-analyzeSingleSampleBoth.R ..Rcheck/tests/testthat/test-analyze_batch.R ..Rcheck/tests/testthat/test-annotateBed.R ..Rcheck/tests/testthat/test-association_analysis.R ..Rcheck/tests/testthat/test-buildDataSetFromGeo.R ..Rcheck/tests/testthat/test-createExcelPivot.R ..Rcheck/tests/testthat/test-createHeatmap.R ..Rcheck/tests/testthat/test-createMultipleBed.R ..Rcheck/tests/testthat/test-create_deltaq.R ..Rcheck/tests/testthat/test-deltaSingleSample.R ..Rcheck/tests/testthat/test-getLesions.R ..Rcheck/tests/testthat/test-getMutations.R ..Rcheck/tests/testthat/test-populationCheck.R ..Rcheck/tests/testthat/test-quantreg_summary.R ..Rcheck/tests/testthat/test-range_beta_values.R ..Rcheck/tests/testthat/test-readMultipleBed.R ..Rcheck/tests/testthat/test-semseeker.R ..Rcheck/tests/testthat/test-sortByCHRandStart.R ..Rcheck/tests/testthat/test-test_match_order.R LICENSE.md R/analyze_batch.R R/analyze_population.R R/analyze_single_sample.R R/analyze_single_sample_both.R R/annotate_bed.R R/apply_stat_model.R R/apply_stat_model_sig.formula.R R/association_analysis.R R/batch_correlation_check.R R/beta_create_pivot.R R/beta_save.R R/beta_single_sample.R R/boot_pvalue_for_lqm.R R/build_data_set_from_geo.R R/close_env.R R/convertTextToNumeric.R R/coverage_analysis.R R/create_excel_pivot.R R/create_excel_pivot_big.R R/create_heatmap.R R/create_multiple_bed.R R/data.R R/data_distribution_info.R R/data_preparation.R R/delta_single_sample.R R/deltaq_get.R R/deltar_get.R R/deltarq_get.R R/dir_check_and_create.R R/dump_sample_as_bed_file.R R/example/example_1.R R/example/example_2.R R/example/example_inference.R R/file_path_build.R R/get_meth_tech.R R/get_pivot.R R/get_session_info.R R/glm_model.R R/inference_file_name.R R/init_env.R R/lesions_get.R R/log_event.R R/manhattan_plot_per_area.R R/mutations_get.R R/pathway_PathfindR.R R/pivot_to_long_format.R R/population_check.R R/probe_features_get.R R/quantreg_model.R R/quantreg_summary.R R/range_beta_values.R R/read_annotated_bed.R R/read_multiple_bed.R R/semseeker.R R/sort_by_chr_and_start.R R/test-helpers.R R/test_match_order.R R/test_model.R R/update_multiple_bed.R R/update_session_info.R R/violin_plot_only_significative_areas.R R/zzz.R README.Rmd README.md man/PROBES.Rd man/PROBES_CHR_CHR.Rd man/analyze_population.Rd man/analyze_single_sample.Rd man/annotate_bed.Rd man/apply_stat_model.Rd man/association_analysis.Rd man/build_data_set_from_geo.Rd man/compute_qr_beta_boot_p.Rd man/compute_quantreg_beta_boot_np.Rd man/create_heatmap.Rd man/data_preparation.Rd man/delta_single_sample.Rd man/deltar_single_sample.Rd man/dir_check_and_create.Rd man/dump_sample_as_bed_file.Rd man/glm_model.Rd man/init_env.Rd man/manhattan_plot_per_area.Rd man/mutations_get.Rd man/pivot_to_long_format.Rd man/pp_tot.Rd man/quantreg_model.Rd man/quantreg_summary.Rd man/range_beta_values.Rd man/read_multiple_bed.Rd man/semseeker.Rd man/sort_by_chr_and_start.Rd man/test_match_order.Rd man/test_model.Rd renv/activate.R tests/tastthat.R tests/testthat/setup.R tests/testthat/test-0-init_env.R tests/testthat/test-1-beta.R tests/testthat/test-1-convertTextToNumeric.R tests/testthat/test-1-get_meth_tech.R tests/testthat/test-1-populationCheck.R tests/testthat/test-1-range_beta_values.R tests/testthat/test-1-sortByCHRandStart.R tests/testthat/test-1-test_match_order.R tests/testthat/test-2-analyzeSingleSample.R tests/testthat/test-2-coverage-analysis.R tests/testthat/test-2-deltaSingleSample.R tests/testthat/test-2-deltar_single_sample.R tests/testthat/test-2-getLesions.R tests/testthat/test-2-getMutations.R tests/testthat/test-3-analyzePopulation.R tests/testthat/test-3-analyze_batch.R tests/testthat/test-4-annotateBed.R tests/testthat/test-4-createMultipleBed.R tests/testthat/test-4-readMultipleBed.R tests/testthat/test-5-createExcelPivot.R tests/testthat/test-5-deltaq_get.R tests/testthat/test-5-deltarq_get.R tests/testthat/to_review/test-apply_stat_model_sig_formula.R tests/testthat/to_review/test-association_analysis.R tests/testthat/to_review/test-buildDataSetFromGeo.R tests/testthat/to_review/test-createHeatmap.R tests/testthat/to_review/test-inference_file_name.R tests/testthat/to_review/test-quantreg_summary.R tests/testthat/to_review/test-semseeker.R