GitHub - BU-BMSIP/White_sTF_PROseq: BMSIP project in Khalil lab for measuring synthetic transcription factor kinetics with PROseq

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
modules		modules
notes		notes
papers		papers
scripts		scripts
traces		traces
.gitignore		.gitignore
2xtims-p65_summary.csv		2xtims-p65_summary.csv
READ_ME.md		READ_ME.md
Snakefile		Snakefile
analyze_strand_bias.py		analyze_strand_bias.py
cluster_config.yaml		cluster_config.yaml
condition_a_summary.csv		condition_a_summary.csv
condition_b_summary.csv		condition_b_summary.csv
config.yaml		config.yaml
convert_s19_bam_to_bed.sh		convert_s19_bam_to_bed.sh
correct_proseq_analysis.sh		correct_proseq_analysis.sh
diagnose_missing_sample.sh		diagnose_missing_sample.sh
diagnostic_traces.png		diagnostic_traces.png
diagnostic_traces_all_samples.png		diagnostic_traces_all_samples.png
environment.yml		environment.yml
experimental_design.csv		experimental_design.csv
export_for_string.r		export_for_string.r
final_publication_style.png		final_publication_style.png
fix_step6.sh		fix_step6.sh
git_ignore.sh		git_ignore.sh
load_modules.sh		load_modules.sh
main.nf		main.nf
multi_condition_proseq_traces.png		multi_condition_proseq_traces.png
multi_condition_traces.py		multi_condition_traces.py
nextflow.config		nextflow.config
original_vs_corrected_comparison.csv		original_vs_corrected_comparison.csv
original_vs_corrected_traces.png		original_vs_corrected_traces.png
p65_summary.csv		p65_summary.csv
p65_vs_2xTIMs_p65_proseq_traces.png		p65_vs_2xTIMs_p65_proseq_traces.png
panel_E_dual_gene_analysis.png		panel_E_dual_gene_analysis.png
panel_e_dual_gene_analysis.py		panel_e_dual_gene_analysis.py
plasmid_cassette_R2_signal.png		plasmid_cassette_R2_signal.png
plasmid_cassette_signal.png		plasmid_cassette_signal.png
plasmid_proseq_signal.png		plasmid_proseq_signal.png
plot_all_samples.py		plot_all_samples.py
plot_corrected_traces.py		plot_corrected_traces.py
plot_proseq_traces.py		plot_proseq_traces.py
publication_yaxis_matching.py		publication_yaxis_matching.py
relevant_rnaseq_analysis.r		relevant_rnaseq_analysis.r
run_proseq.sh		run_proseq.sh
sample_summary_statistics.csv		sample_summary_statistics.csv
samples_R1_only.csv		samples_R1_only.csv
samplesheet.csv		samplesheet.csv
samplesheet_R1_only.csv		samplesheet_R1_only.csv
strand_bias_analysis.png		strand_bias_analysis.png