Files in CyanolabFreiburg/rifi

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

.BBSoptions

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/.ipynb_checkpoints/Imports-checkpoint.r R/.ipynb_checkpoints/TUgether-checkpoint.r R/.ipynb_checkpoints/annotation_plot-checkpoint.r R/.ipynb_checkpoints/apply_Ttest_delay-checkpoint.r R/.ipynb_checkpoints/apply_ancova-checkpoint.r R/.ipynb_checkpoints/apply_event_position-checkpoint.r R/.ipynb_checkpoints/apply_manova-checkpoint.r R/.ipynb_checkpoints/apply_t_test-checkpoint.r R/.ipynb_checkpoints/apply_t_test_ti-checkpoint.r R/.ipynb_checkpoints/check_input-checkpoint.r R/.ipynb_checkpoints/dataframe_summary-checkpoint.r R/.ipynb_checkpoints/dataframe_summary_TI-checkpoint.r R/.ipynb_checkpoints/dataframe_summary_events-checkpoint.r R/.ipynb_checkpoints/dataframe_summary_events_HL_int-checkpoint.r R/.ipynb_checkpoints/dataframe_summary_events_ps_itss-checkpoint.r R/.ipynb_checkpoints/dataframe_summary_events_velocity-checkpoint.r R/.ipynb_checkpoints/empty_data_negative-checkpoint.r R/.ipynb_checkpoints/empty_data_positive-checkpoint.r R/.ipynb_checkpoints/event_dataframe-checkpoint.r R/.ipynb_checkpoints/filtration_below_backg-checkpoint.r R/.ipynb_checkpoints/finding_PDD-checkpoint.r R/.ipynb_checkpoints/finding_TI-checkpoint.r R/.ipynb_checkpoints/fold_change-checkpoint.r R/.ipynb_checkpoints/fragment_HL-checkpoint.r R/.ipynb_checkpoints/fragment_HL_pen-checkpoint.r R/.ipynb_checkpoints/fragment_TI-checkpoint.r R/.ipynb_checkpoints/fragment_TI_pen-checkpoint.r R/.ipynb_checkpoints/fragment_delay-checkpoint.r R/.ipynb_checkpoints/fragment_delay_pen-checkpoint.r R/.ipynb_checkpoints/fragment_inty-checkpoint.r R/.ipynb_checkpoints/fragment_inty_pen-checkpoint.r R/.ipynb_checkpoints/function_df_summary-checkpoint.r R/.ipynb_checkpoints/function_fold_change-checkpoint.r R/.ipynb_checkpoints/functions_df_events-checkpoint.r R/.ipynb_checkpoints/functions_gff-checkpoint.r R/.ipynb_checkpoints/functions_plot_fit-checkpoint.r R/.ipynb_checkpoints/functions_scoring-checkpoint.r R/.ipynb_checkpoints/functions_t-test_manova-checkpoint.r R/.ipynb_checkpoints/functions_visualization-checkpoint.r R/.ipynb_checkpoints/generic_filter_BG-checkpoint.r R/.ipynb_checkpoints/gff3_preprocessing-checkpoint.r R/.ipynb_checkpoints/globals-checkpoint.r R/.ipynb_checkpoints/make_df-checkpoint.r R/.ipynb_checkpoints/make_pen-checkpoint.r R/.ipynb_checkpoints/negative_strand_function-checkpoint.r R/.ipynb_checkpoints/nls2_fit-checkpoint.r R/.ipynb_checkpoints/positive_strand_function-checkpoint.r R/.ipynb_checkpoints/predict_ps_itss-checkpoint.r R/.ipynb_checkpoints/rifi_fit-checkpoint.r R/.ipynb_checkpoints/rifi_fragmentation-checkpoint.r R/.ipynb_checkpoints/rifi_penalties-checkpoint.r R/.ipynb_checkpoints/rifi_preprocess-checkpoint.r R/.ipynb_checkpoints/rifi_stats-checkpoint.r R/.ipynb_checkpoints/rifi_summary-checkpoint.r R/.ipynb_checkpoints/rifi_visualization-checkpoint.r R/.ipynb_checkpoints/rifi_wrapper-checkpoint.r R/.ipynb_checkpoints/segment_pos-checkpoint.r R/.ipynb_checkpoints/utils-checkpoint.r R/.ipynb_checkpoints/viz_pen_obj-checkpoint.r R/Imports.r R/TI_fit.r R/TUgether.r R/annotation_plot.r R/apply_Ttest_delay.r R/apply_ancova.r R/apply_event_position.r R/apply_manova.r R/apply_t_test.r R/apply_t_test_ti.r R/check_input.r R/data.r R/dataframe_summary.r R/dataframe_summary_TI.r R/dataframe_summary_events.r R/dataframe_summary_events_HL_int.r R/dataframe_summary_events_ps_itss.r R/dataframe_summary_events_velocity.r R/empty_data_negative.r R/empty_data_positive.r R/event_dataframe.r R/filtration_below_backg.r R/finding_PDD.r R/finding_TI.r R/fold_change.r R/fragment_HL.r R/fragment_HL_pen.r R/fragment_TI.r R/fragment_TI_pen.r R/fragment_delay.r R/fragment_delay_pen.r R/fragment_inty.r R/fragment_inty_pen.r R/function_df_summary.r R/function_fold_change.r R/functions_df_events.r R/functions_gff.r R/functions_plot_fit.r R/functions_scoring.r R/functions_t-test_manova.r R/functions_visualization.r R/generic_filter_BG.r R/gff3_preprocessing.r R/globals.r R/make_df.r R/make_pen.r R/negative_strand_function.r R/nls2_fit.r R/positive_strand_function.r R/predict_ps_itss.r R/rifi_fit.r R/rifi_fragmentation.r R/rifi_penalties.r R/rifi_preprocess.r R/rifi_stats.r R/rifi_summary.r R/rifi_visualization.r R/rifi_wrapper.r R/segment_pos.r R/utils.r R/viz_pen_obj.r README.md

data/example_input_e_coli.RData

data/example_input_minimal.RData

data/example_input_synechocystis_6803.RData

data/fit_e_coli.RData

data/fit_minimal.RData

data/fit_synechocystis_6803.RData

data/fragmentation_e_coli.RData

data/fragmentation_minimal.RData

data/fragmentation_synechocystis_6803.RData

data/penalties_e_coli.RData

data/penalties_minimal.RData

data/penalties_synechocystis_6803.RData

data/preprocess_e_coli.RData

data/preprocess_minimal.RData

data/preprocess_synechocystis_6803.RData

data/res_minimal.RData

data/stats_e_coli.RData

data/stats_minimal.RData

data/stats_synechocystis_6803.RData

data/summary_e_coli.RData

data/summary_minimal.RData

data/summary_synechocystis_6803.RData

data/wrapper_e_coli.RData

data/wrapper_minimal.RData

data/wrapper_summary_synechocystis_6803.RData

inst/NEWS.md

inst/extdata/data_needed

inst/extdata/genome_fragments_e_coli.pdf inst/extdata/genome_fragments_synechocystis_6803.pdf

inst/extdata/gff_e_coli.gff3.gz

inst/extdata/gff_synechocystis_6803.gff.gz

man/TI_fit.Rd man/TUgether.Rd man/apply_Ttest_delay.Rd man/apply_ancova.Rd man/apply_event_position.Rd man/apply_manova.Rd man/apply_t_test.Rd man/apply_t_test_ti.Rd man/check_input.Rd man/dataframe_summary.Rd man/dataframe_summary_TI.Rd man/dataframe_summary_events.Rd man/dataframe_summary_events_HL_int.Rd man/dataframe_summary_events_ps_itss.Rd man/dataframe_summary_events_velocity.Rd man/event_dataframe.Rd man/example_input_e_coli.Rd man/example_input_minimal.Rd man/example_input_synechocystis_6803.Rd man/finding_PDD.Rd man/finding_TI.Rd man/fit_e_coli.Rd man/fit_minimal.Rd man/fit_synechocystis_6803.Rd man/fold_change.Rd man/fragment_HL.Rd man/fragment_TI.Rd man/fragment_delay.Rd man/fragment_inty.Rd man/fragmentation_e_coli.Rd man/fragmentation_minimal.Rd man/fragmentation_synechocystis_6803.Rd man/gff3_preprocess.Rd man/make_df.Rd man/make_pen.Rd man/nls2_fit.Rd man/penalties_e_coli.Rd man/penalties_minimal.Rd man/penalties_synechocystis_6803.Rd man/predict_ps_itss.Rd man/preprocess_e_coli.Rd man/preprocess_minimal.Rd man/preprocess_synechocystis_6803.Rd man/res_minimal.Rd man/rifi_fit.Rd man/rifi_fragmentation.Rd man/rifi_penalties.Rd man/rifi_preprocess.Rd man/rifi_stats.Rd man/rifi_summary.Rd man/rifi_visualization.Rd man/rifi_wrapper.Rd man/segment_pos.Rd man/stats_e_coli.Rd man/stats_minimal.Rd man/stats_synechocystis_6803.Rd man/summary_e_coli.Rd man/summary_minimal.Rd man/summary_synechocystis_6803.Rd man/viz_pen_obj.Rd man/wrapper_e_coli.Rd man/wrapper_minimal.Rd man/wrapper_summary_synechocystis_6803.Rd vignettes/.ipynb_checkpoints/vignette-checkpoint.Rmd

vignettes/.ipynb_checkpoints/vignette-checkpoint.html

vignettes/TIPlot.png

vignettes/bad_penalties.png

vignettes/events.png

vignettes/fit_models.png

vignettes/genome_fragments_plot.png

vignettes/genome_plot_1.png

vignettes/genome_plot_2.png

vignettes/header.html

vignettes/highValues.png

vignettes/hirarchy3.png

vignettes/longSegments.png

vignettes/miniSegments.png

vignettes/nls2Plot.png

vignettes/penalty.png

vignettes/principle.png

vignettes/references.bib

vignettes/vignette.Rmd

CyanolabFreiburg/rifi documentation built on May 7, 2023, 7:53 p.m.