GitHub - algaebrown/Mudskipper_analysis: Analysis for tool Mudskipper, built to analyze multiplex CLIP

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Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
.gitignore		.gitignore
0_Basic_statistics.ipynb		0_Basic_statistics.ipynb
0_Make_fastq_csv.ipynb		0_Make_fastq_csv.ipynb
0_Raw_data_visualization.ipynb		0_Raw_data_visualization.ipynb
1_DMN_analysis.ipynb		1_DMN_analysis.ipynb
1_Evaluate_all_model_and_bg.ipynb		1_Evaluate_all_model_and_bg.ipynb
1_compare_BBMCC_DMM.ipynb		1_compare_BBMCC_DMM.ipynb
1_visualize_motif.ipynb		1_visualize_motif.ipynb
2_eCLIP_common_bg.ipynb		2_eCLIP_common_bg.ipynb
2_smallRNA_repeat_binding.ipynb		2_smallRNA_repeat_binding.ipynb
2_softmask_benchmark.ipynb		2_softmask_benchmark.ipynb
2_softmask_visualize.ipynb		2_softmask_visualize.ipynb
3_correlate_SF3B4_LR_w_U2_energy.ipynb		3_correlate_SF3B4_LR_w_U2_energy.ipynb
3_score_splicin-A3SS.ipynb		3_score_splicin-A3SS.ipynb
3_score_splicing-A5SS.ipynb		3_score_splicing-A5SS.ipynb
3_splicing_analysis_RBFOX2-DMN.ipynb		3_splicing_analysis_RBFOX2-DMN.ipynb
4_PCA_of_backgrounds.ipynb		4_PCA_of_backgrounds.ipynb
4_singleplex_BBM-gc_aware_RBFOX2.ipynb		4_singleplex_BBM-gc_aware_RBFOX2.ipynb
4_singleplex_BBM-gc_aware_SLBP.ipynb		4_singleplex_BBM-gc_aware_SLBP.ipynb
5_cell_type_reps_RBFOX2_splicing.ipynb		5_cell_type_reps_RBFOX2_splicing.ipynb
5_shared_binding_and_example_L2.ipynb		5_shared_binding_and_example_L2.ipynb
6_Metadensity_DMN_peaks.ipynb		6_Metadensity_DMN_peaks.ipynb
7_Functional_variants.ipynb		7_Functional_variants.ipynb
8_Clinvar_variants.ipynb		8_Clinvar_variants.ipynb
S1_model_fit.ipynb		S1_model_fit.ipynb
S2_label_with_old_pipeline-1rep.ipynb		S2_label_with_old_pipeline-1rep.ipynb
S2_label_with_old_pipeline.ipynb		S2_label_with_old_pipeline.ipynb
S2_label_with_skipper.ipynb		S2_label_with_skipper.ipynb
S3_DMN_analysis-ncomp_AUPRC.ipynb		S3_DMN_analysis-ncomp_AUPRC.ipynb
S3_output_analysis.ipynb		S3_output_analysis.ipynb
S3_output_params.ipynb		S3_output_params.ipynb
S4_DMN_analysis-fc_AUPRC.ipynb		S4_DMN_analysis-fc_AUPRC.ipynb
S4_fraction_read_cutoff.ipynb		S4_fraction_read_cutoff.ipynb
S5_DPMM.ipynb		S5_DPMM.ipynb
S5_DPMM_R.ipynb		S5_DPMM_R.ipynb
S5_DPMM_pyro-tutorial.ipynb		S5_DPMM_pyro-tutorial.ipynb
S5_DPMM_pyro.ipynb		S5_DPMM_pyro.ipynb
S6_Find_consecutive_window_CLIPper.ipynb		S6_Find_consecutive_window_CLIPper.ipynb
S6_consecutive_window.ipynb		S6_consecutive_window.ipynb
debug_QC.ipynb		debug_QC.ipynb
entropy.ipynb		entropy.ipynb
plot_params.py		plot_params.py
prepare_dl.ipynb		prepare_dl.ipynb
try_fit_null.ipynb		try_fit_null.ipynb
try_fit_null_tfp.ipynb		try_fit_null_tfp.ipynb