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ami
ami
 
 
figure1a_comparison_between_chipseq_and_chipnexus
figure1a_comparison_between_chipseq_and_chipnexus
 
 
figure1c_1d_basal_factors_and_polii_under_control_and_triptolide_treated_condition
figure1c_1d_basal_factors_and_polii_under_control_and_triptolide_treated_condition
 
 
figure2a_triptolide_time_course_single_gene_example
figure2a_triptolide_time_course_single_gene_example
 
 
figure2b_2c_2d_calculating_paused_polii_half_life
figure2b_2c_2d_calculating_paused_polii_half_life
 
 
figure2e_mRNA_and_pausing_index
figure2e_mRNA_and_pausing_index
 
 
figure2f_and_2g_nelf_and_polii_loss_afer_nelf_kd
figure2f_and_2g_nelf_and_polii_loss_afer_nelf_kd
 
 
figure2h_promoter_element_enrichment
figure2h_promoter_element_enrichment
 
 
figure3a_3b_initiating_polii
figure3a_3b_initiating_polii
 
 
figure3c_3d_basal_factors_at_genes_with_different_half_life
figure3c_3d_basal_factors_at_genes_with_different_half_life
 
 
figure4a_4b_initiating_polii_after_fP_DRB_treatment
figure4a_4b_initiating_polii_after_fP_DRB_treatment
 
 
half_life_extended_table
half_life_extended_table
 
 
html_include
html_include
 
 
html_support
html_support
 
 
pipeline
pipeline
 
 
rdata
rdata
 
 
sample_report
sample_report
 
 
shared_code
shared_code
 
 
supplementary1_compare_replicates
supplementary1_compare_replicates
 
 
supplementary2_basal_factors_and_polii_peak_position
supplementary2_basal_factors_and_polii_peak_position
 
 
supplementary3_human_tbp
supplementary3_human_tbp
 
 
supplementary4_triptolide_concentration
supplementary4_triptolide_concentration
 
 
supplementary5_tfiib
supplementary5_tfiib
 
 
supplementary7_polii_footprint_after_FP_and_DRB
supplementary7_polii_footprint_after_FP_and_DRB
 
 
README.md
README.md
 
 
Supplementary2_basal_factors_and_polii_peak_position.Rmd
Supplementary2_basal_factors_and_polii_peak_position.Rmd
 
 
Supplementary2_basal_factors_and_polii_peak_position.html
Supplementary2_basal_factors_and_polii_peak_position.html
 
 
_output.yaml
_output.yaml
 
 
figure1a_comparison_between_chipseq_and_chipnexus.Rmd
figure1a_comparison_between_chipseq_and_chipnexus.Rmd
 
 
figure1a_comparison_between_chipseq_and_chipnexus.html
figure1a_comparison_between_chipseq_and_chipnexus.html
 
 
figure1c_1d_basal_factors_and_polii_under_control_and_triptolide_treated_condition.Rmd
figure1c_1d_basal_factors_and_polii_under_control_and_triptolide_treated_condition.Rmd
 
 
figure1c_1d_basal_factors_and_polii_under_control_and_triptolide_treated_condition.html
figure1c_1d_basal_factors_and_polii_under_control_and_triptolide_treated_condition.html
 
 
figure2a_triptolide_time_course_single_gene_example.Rmd
figure2a_triptolide_time_course_single_gene_example.Rmd
 
 
figure2a_triptolide_time_course_single_gene_example.html
figure2a_triptolide_time_course_single_gene_example.html
 
 
figure2b_2c_2d_calculating_paused_polii_half_life.Rmd
figure2b_2c_2d_calculating_paused_polii_half_life.Rmd
 
 
figure2b_2c_2d_calculating_paused_polii_half_life.html
figure2b_2c_2d_calculating_paused_polii_half_life.html
 
 
figure2e_mRNA_and_pausing_index.Rmd
figure2e_mRNA_and_pausing_index.Rmd
 
 
figure2e_mRNA_and_pausing_index.html
figure2e_mRNA_and_pausing_index.html
 
 
figure2f_and_2g_nelf_and_polii_loss_afer_nelf_kd.Rmd
figure2f_and_2g_nelf_and_polii_loss_afer_nelf_kd.Rmd
 
 
figure2f_and_2g_nelf_and_polii_loss_afer_nelf_kd.html
figure2f_and_2g_nelf_and_polii_loss_afer_nelf_kd.html
 
 
figure2h_promoter_element_enrichment.Rmd
figure2h_promoter_element_enrichment.Rmd
 
 
figure2h_promoter_element_enrichment.html
figure2h_promoter_element_enrichment.html
 
 
figure3a_3b_initiating_polii.Rmd
figure3a_3b_initiating_polii.Rmd
 
 
figure3a_3b_initiating_polii.html
figure3a_3b_initiating_polii.html
 
 
figure3c_3d_basal_factors_at_gnees_with_different_half_life.Rmd
figure3c_3d_basal_factors_at_gnees_with_different_half_life.Rmd
 
 
figure3c_3d_basal_factors_at_gnees_with_different_half_life.html
figure3c_3d_basal_factors_at_gnees_with_different_half_life.html
 
 
figure4a_4b_initiating_polii_after_flavopiridol_treatment.Rmd
figure4a_4b_initiating_polii_after_flavopiridol_treatment.Rmd
 
 
figure4a_4b_initiating_polii_after_flavopiridol_treatment.html
figure4a_4b_initiating_polii_after_flavopiridol_treatment.html
 
 
half_life_extended_table.Rmd
half_life_extended_table.Rmd
 
 
half_life_extended_table.html
half_life_extended_table.html
 
 
half_life_extended_table.txt
half_life_extended_table.txt
 
 
promoter_elements.txt
promoter_elements.txt
 
 
sample_list.csv
sample_list.csv
 
 
sample_report.Rmd
sample_report.Rmd
 
 
sample_report.html
sample_report.html
 
 
sample_report.txt
sample_report.txt
 
 
supplementary1_compare_replicates.Rmd
supplementary1_compare_replicates.Rmd
 
 
supplementary1_compare_replicates.html
supplementary1_compare_replicates.html
 
 
supplementary3_human_tbp.Rmd
supplementary3_human_tbp.Rmd
 
 
supplementary3_human_tbp.html
supplementary3_human_tbp.html
 
 
supplementary4_triptolide_concentration.Rmd
supplementary4_triptolide_concentration.Rmd
 
 
supplementary4_triptolide_concentration.html
supplementary4_triptolide_concentration.html
 
 
supplementary5_tfiib.Rmd
supplementary5_tfiib.Rmd
 
 
supplementary5_tfiib.html
supplementary5_tfiib.html
 
 
supplementary7_polii_footprint_after_FP_and_DRB.Rmd
supplementary7_polii_footprint_after_FP_and_DRB.Rmd
 
 
supplementary7_polii_footprint_after_FP_and_DRB.html
supplementary7_polii_footprint_after_FP_and_DRB.html
 
 
tss_reannotation.Rmd
tss_reannotation.Rmd
 
 
tss_reannotation.html
tss_reannotation.html
 
 

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Shao initiation and Pol II pausing paper

Analysis code for Shao and Zeitlinger 2017 manuscript

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