Preview

gosianow-DRIMSeq_paper_analyses-847675d
- .gitignore
  
  61 Bytes
- README.md
  
  717 Bytes
- analysis_brooks_pasilla
  - brooks_dexseq_run.R
    
    5.0 kB
  - brooks_download.R
    
    4.9 kB
  - brooks_drimseq_0_3_3_auto_moderation.R
    
    2.4 kB
  - brooks_drimseq_0_3_3_comparison.R
    
    15.7 kB
  - brooks_drimseq_0_3_3_comparison_models.R
    
    4.6 kB
  - brooks_drimseq_0_3_3_comparison_plots.R
    
    6.1 kB
  - brooks_drimseq_0_3_3_comparison_summary.R
    
    5.3 kB
  - brooks_drimseq_0_3_3_positive_controls.R
    
    7.1 kB
  - brooks_drimseq_0_3_3_positive_controls_gviz.R
    
    5.0 kB
  - brooks_drimseq_0_3_3_positive_controls_plots.R
    
    6.0 kB
  - brooks_drimseq_0_3_3_positive_controls_summary.R
    
    5.3 kB
  - brooks_drimseq_0_3_3_run.R
    
    8.6 kB
  - brooks_htseq.R
    
    2.6 kB
  - brooks_kallisto.R
    
    6.7 kB
  - brooks_kallisto_filter_gtf.R
    
    5.7 kB
  - brooks_mds.R
    
    3.0 kB
  - brooks_run.sh
    
    11.2 kB
  - brooks_validated_genes.R
    
    2.1 kB
  - colors.R
    
    2.6 kB
- analysis_geuvadis
  - colors.R
    
    2.0 kB
  - geuvadis_drimseq_0_3_3_biol_comparison_plots.R
    
    24.8 kB
  - geuvadis_drimseq_0_3_3_comparison_permutations.R
    
    18.3 kB
  - geuvadis_drimseq_0_3_3_comparison_plots.R
    
    7.6 kB
  - geuvadis_drimseq_0_3_3_positive_controls.R
    
    9.2 kB
  - geuvadis_drimseq_0_3_3_positive_controls_gviz.R
    
    5.2 kB
  - geuvadis_drimseq_0_3_3_run_permutations.R
    
    8.6 kB
  - geuvadis_run.sh
    
    11.4 kB
  - geuvadis_sqtlseeker_2_1.R
    
    9.8 kB
  - geuvadis_sqtlseeker_2_1_drimseq_counts.R
    
    10.5 kB
  - prepare_data.R
    
    7.7 kB
  - prepare_validated_sqtls.R
    
    14.1 kB
- analysis_kim_adenocarcinoma
  - colors.R
    
    2.6 kB
  - kim_dexseq_run.R
    
    5.7 kB
  - kim_download.R
    
    4.1 kB
  - kim_drimseq_0_3_3_auto_moderation.R
    
    2.4 kB
  - kim_drimseq_0_3_3_comparison.R
    
    15.7 kB
  - kim_drimseq_0_3_3_comparison_models.R
    
    4.5 kB
  - kim_drimseq_0_3_3_comparison_plots.R
    
    6.1 kB
  - kim_drimseq_0_3_3_comparison_summary.R
    
    5.3 kB
  - kim_drimseq_0_3_3_run.R
    
    8.7 kB
  - kim_htseq.R
    
    3.6 kB
  - kim_kallisto.R
    
    4.3 kB
  - kim_kallisto_filter_gtf.R
    
    3.9 kB
  - kim_mds.R
    
    2.9 kB
  - kim_run.sh
    
    7.5 kB
- help_functions
  - dmDS_auto_moderation_diagnostics.R
    
    20.0 kB
  - dmDS_lr_contribution.R
    
    2.4 kB
  - dm_plotCAT.R
    
    3.8 kB
  - dm_plotOverlaps.R
    
    3.8 kB
  - dm_plotROCx.R
    
    6.4 kB
  - dm_plotTPRFDR.R
    
    4.7 kB
- simulations_dm
  - core_dispersion_plots_run.R
    
    10.2 kB
  - core_dispersion_run.R
    
    6.7 kB
  - core_dispersion_run.sh
    
    3.0 kB
  - core_fp_plots_run.R
    
    22.1 kB
  - core_fp_run.R
    
    11.1 kB
  - core_fp_run.sh
    
    7.6 kB
  - dispersion_plots_run.R
    
    12.1 kB
  - dispersion_run.R
    
    7.6 kB
  - dispersion_run.sh
    
    4.1 kB
  - dm_parameters_run.R
    
    20.6 kB
  - dm_parameters_run.sh
    
    1.1 kB
  - dm_simulate.R
    
    1.9 kB
  - filtering_and_moderation_real_plots_run.R
    
    14.4 kB
  - filtering_and_moderation_real_run.R
    
    9.1 kB
  - filtering_and_moderation_real_run.sh
    
    5.3 kB
  - filtering_and_moderation_sim_plots_run.R
    
    15.3 kB
  - filtering_and_moderation_sim_run.R
    
    7.1 kB
  - filtering_and_moderation_sim_run.sh
    
    1.9 kB
  - filtering_sim_plots_run.R
    
    14.4 kB
  - filtering_sim_run.R
    
    5.6 kB
  - filtering_sim_run.sh
    
    2.5 kB
  - moderation_real_auto_plots_run.R
    
    15.5 kB
  - moderation_real_auto_run.R
    
    6.6 kB
  - moderation_real_auto_run.sh
    
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  - moderation_real_plots_run.R
    
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  - moderation_real_run.R
    
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  - moderation_real_run.sh
    
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  - proportions_and_moderation_sim_plots_run.R
    
    12.4 kB
  - proportions_and_moderation_sim_run.R
    
    7.2 kB
  - proportions_and_moderation_sim_run.sh
    
    3.4 kB
  - proportions_sim_f_investigate_results.R
    
    13.2 kB
  - proportions_sim_f_plots_run.R
    
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  - proportions_sim_f_run.R
    
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  - proportions_sim_f_run.sh
    
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  - proportions_sim_plots_run.R
    
    14.4 kB
  - proportions_sim_run.R
    
    8.0 kB
  - proportions_sim_run.sh
    
    2.4 kB
- simulations_sim5
  - colors.R
    
    2.6 kB
  - sim5_dexseq_run.R
    
    4.1 kB
  - sim5_drimseq_auto_moderation.R
    
    2.4 kB
  - sim5_drimseq_comparison.R
    
    24.2 kB
  - sim5_drimseq_comparison_combined.R
    
    15.3 kB
  - sim5_drimseq_comparison_filtering.R
    
    9.8 kB
  - sim5_drimseq_investigate_results.R
    
    11.1 kB
  - sim5_drimseq_run.R
    
    7.1 kB
  - sim5_histograms_of_features.R
    
    5.2 kB
  - sim5_htseq.R
    
    2.7 kB
  - sim5_kallisto.R
    
    4.6 kB
  - sim5_kallisto_filter_gtf_fa.R
    
    5.2 kB
  - sim5_run.sh
    
    11.8 kB

gosianow/DRIMSeq_paper_analyses-2.0.zip