bremdata

These are custom scripts for data analysis in my PhD project, including scripts for bioRxiv doi 10.1101/2020.08.31.275453. Essentially, this is where I backup my work, and link it to share with teammates. For final scripts used in my publications, visit https://github.com/melanieabrams-pub/

Name		Name	Last commit message	Last commit date
Latest commit History 155 Commits
0associate_barcodes.py		0associate_barcodes.py
10effect_size.py		10effect_size.py
10effect_size_brs_insert_ratios.py		10effect_size_brs_insert_ratios.py
10effect_size_insert_ratios.py		10effect_size_insert_ratios.py
10effect_size_rhseqv2.py		10effect_size_rhseqv2.py
10effect_size_v2.py		10effect_size_v2.py
1annotate_vcfs.py		1annotate_vcfs.py
2fANOVA_for_doseresponse.py		2fANOVA_for_doseresponse.py
2fanova_analyseresults.py		2fanova_analyseresults.py
2total_reads_and_normalize_rhseqv2.py		2total_reads_and_normalize_rhseqv2.py
3remove_NC_and_plasmid_inserts_rhseqv2.py		3remove_NC_and_plasmid_inserts_rhseqv2.py
4one_tr.py		4one_tr.py
4reformat_single_techrep_rhseqv2.py		4reformat_single_techrep_rhseqv2.py
5combine_bio_reps_MBA.py		5combine_bio_reps_MBA.py
5combine_bio_reps_MBA_nonzeros.py		5combine_bio_reps_MBA_nonzeros.py
5combine_bioreps_rhseqv2.py		5combine_bioreps_rhseqv2.py
6filter_inserts_rhseqv2.py		6filter_inserts_rhseqv2.py
6filter_inserts_uncollapsedMBA.py		6filter_inserts_uncollapsedMBA.py
6filter_inserts_uncollapsedMBA_debug.py		6filter_inserts_uncollapsedMBA_debug.py
7fitness_ratios_rhseqv2.py		7fitness_ratios_rhseqv2.py
7fitness_ratios_uncollapsedMBA.py		7fitness_ratios_uncollapsedMBA.py
7fitness_ratios_uncollapsedMBA_nozeros_unpaired.py		7fitness_ratios_uncollapsedMBA_nozeros_unpaired.py
7fitness_ratios_uncollapsedMBA_nozeros_unpaired_brthreshold_v2.py		7fitness_ratios_uncollapsedMBA_nozeros_unpaired_brthreshold_v2.py
7fitness_ratios_uncollapsedMBA_unpaired.py		7fitness_ratios_uncollapsedMBA_unpaired.py
7fitness_ratios_uncollapsedMBA_unpaired_median.py		7fitness_ratios_uncollapsedMBA_unpaired_median.py
8organize_and_filter_genes_ratiocv_uncollapsedMBA.py		8organize_and_filter_genes_ratiocv_uncollapsedMBA.py
8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug.py		8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug.py
8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug_nozeros.py		8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug_nozeros.py
8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug_nozeros_spminmax.py		8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug_nozeros_spminmax.py
8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug_nozeros_v2.py		8organize_and_filter_genes_ratiocv_uncollapsedMBA_debug_nozeros_v2.py
8organize_and_filter_genes_ratiocv_uncollapsedMBA_nozeros.py		8organize_and_filter_genes_ratiocv_uncollapsedMBA_nozeros.py
8organize_and_filter_genes_rhseqv2.py		8organize_and_filter_genes_rhseqv2.py
8organize_and_filter_genes_stdcutoff_uncollapsedMBA.py		8organize_and_filter_genes_stdcutoff_uncollapsedMBA.py
8organize_and_filter_genes_uncollapsedMBA.py		8organize_and_filter_genes_uncollapsedMBA.py
9fisher.py		9fisher.py
9mann_whitney_u_rhseqv2.py		9mann_whitney_u_rhseqv2.py
9mann_whitney_u_uncollapsedMBA_py3_onlyessential.py		9mann_whitney_u_uncollapsedMBA_py3_onlyessential.py
9mann_whitney_u_uncollapsedMBA_py3_testgene.py		9mann_whitney_u_uncollapsedMBA_py3_testgene.py
9mann_whitney_u_uncollapsedMBA_py3_testgene_nonzeros.py		9mann_whitney_u_uncollapsedMBA_py3_testgene_nonzeros.py
9mann_whitney_u_uncollapsedMBA_py3_testgene_nonzeros_recollapsed_br.py		9mann_whitney_u_uncollapsedMBA_py3_testgene_nonzeros_recollapsed_br.py
9mann_whitney_u_uncollapsedMBA_py3_testgene_nonzeros_recollapsed_ins.py		9mann_whitney_u_uncollapsedMBA_py3_testgene_nonzeros_recollapsed_ins.py
9mwurecollapsed.py		9mwurecollapsed.py
9t-test.py		9t-test.py
HITS_37C_2.0_1.1_coeffvarANDreadcutoff_uncollapsedMBA_unpaired_ratiocvfilt_10.0_3.0pcut0pt05spmaxoffby100.fxsizes.txt		HITS_37C_2.0_1.1_coeffvarANDreadcutoff_uncollapsedMBA_unpaired_ratiocvfilt_10.0_3.0pcut0pt05spmaxoffby100.fxsizes.txt
Mabrams_eVOLVER_scripts_2018-10-18.zip		Mabrams_eVOLVER_scripts_2018-10-18.zip
Mabrams_eVOLVER_scripts_2019-6-19.zip		Mabrams_eVOLVER_scripts_2019-6-19.zip
RBseq_Calculate_Fitness_v1.1.4_PB_MAmod.py		RBseq_Calculate_Fitness_v1.1.4_PB_MAmod.py
RBseq_Count_BarCodes_1.0.7_EcoliOutFile.py		RBseq_Count_BarCodes_1.0.7_EcoliOutFile.py
README.md		README.md
RH_2fANOVA_2-5-2019_carlydata.py		RH_2fANOVA_2-5-2019_carlydata.py
alignments_get_only_one_scer_pop.py		alignments_get_only_one_scer_pop.py
amend_s288c_with_vcfs.py		amend_s288c_with_vcfs.py
annotate_with_SGD_csv.py		annotate_with_SGD_csv.py
assign_sampleNames_h12haps.py		assign_sampleNames_h12haps.py
automate_g12test.py		automate_g12test.py
automate_g12test_barseqGenes.py		automate_g12test_barseqGenes.py
automate_g1test.py		automate_g1test.py
automate_g1test_barseqGenes.py		automate_g1test_barseqGenes.py
automate_g2g1test.py		automate_g2g1test.py
barseq_library_coverage.py		barseq_library_coverage.py
barseq_map_and_pool_BLAT_3-19-2020.py		barseq_map_and_pool_BLAT_3-19-2020.py
barseq_map_and_pool_BLAT_3-25-20.py		barseq_map_and_pool_BLAT_3-25-20.py
barseq_map_and_pool_BLAT_4-2-20.py		barseq_map_and_pool_BLAT_4-2-20.py
barseq_merge_only_3-19-20_test-dup.py		barseq_merge_only_3-19-20_test-dup.py
barseq_merge_only_3-25.py		barseq_merge_only_3-25.py
barseq_merge_only_4-2-2020.py		barseq_merge_only_4-2-2020.py
barseq_pool_from_mapped_blat_3-25-2020.py		barseq_pool_from_mapped_blat_3-25-2020.py
barseq_pool_from_mapped_blat_4-2-2020.py		barseq_pool_from_mapped_blat_4-2-2020.py
barseq_pool_from_mapped_reads_3_19_2020.py		barseq_pool_from_mapped_reads_3_19_2020.py
blat_for_cameron.py		blat_for_cameron.py
blat_for_cameron_v2.py		blat_for_cameron_v2.py
buildAnnotationFile_vcfIDs.py		buildAnnotationFile_vcfIDs.py
calc_avg_depth.py		calc_avg_depth.py
cdf_plot_37in36.py		cdf_plot_37in36.py
commands_for_rhseqpipeline_analysis.py		commands_for_rhseqpipeline_analysis.py
commands_for_rhseqpipeline_analysis_with_zeros_v2.py		commands_for_rhseqpipeline_analysis_with_zeros_v2.py
compare_effectsize_barcoded-rh-seq_and_carly-rh-seq.py		compare_effectsize_barcoded-rh-seq_and_carly-rh-seq.py
compare_ins_per_kb_v2.py		compare_ins_per_kb_v2.py
compute_unpaired_T-test_thermo_rbseq_MA.py		compute_unpaired_T-test_thermo_rbseq_MA.py
convert_poolcount_to_fastqpooledreadsclean.py		convert_poolcount_to_fastqpooledreadsclean.py
convert_poolcount_to_fastqpooledreadsclean_36C.py		convert_poolcount_to_fastqpooledreadsclean_36C.py
convert_poolcount_to_fastqpooledreadsclean_37C.py		convert_poolcount_to_fastqpooledreadsclean_37C.py
convert_poolcount_to_fastqpooledreadsclean_rhseqv2.py		convert_poolcount_to_fastqpooledreadsclean_rhseqv2.py
convert_poolcount_to_fastqpooledreadsclean_v2.py		convert_poolcount_to_fastqpooledreadsclean_v2.py
convert_scripts_to_py3.py		convert_scripts_to_py3.py
density_plot_allobservations_fitnessfx_v3.py		density_plot_allobservations_fitnessfx_v3.py
density_plot_python.py		density_plot_python.py
density_plot_python_fxsize.py		density_plot_python_fxsize.py
density_plot_python_fxsize_44goi_inCarlyData.py		density_plot_python_fxsize_44goi_inCarlyData.py
density_plot_python_fxsize_carly8.py		density_plot_python_fxsize_carly8.py
density_plot_python_fxsize_goi.py		density_plot_python_fxsize_goi.py
density_plot_python_fxsize_unfiltered_topfx.py		density_plot_python_fxsize_unfiltered_topfx.py
density_plot_replicates_fitnessfx_fromJeffExcel.py		density_plot_replicates_fitnessfx_fromJeffExcel.py
density_plot_replicates_fitnessfx_fromJeffExcel_v2.py		density_plot_replicates_fitnessfx_fromJeffExcel_v2.py
density_plot_replicates_fitnessfx_v3.py		density_plot_replicates_fitnessfx_v3.py
density_plot_separate_replicates_fitnessfx_v3.py		density_plot_separate_replicates_fitnessfx_v3.py
density_plot_separate_replicates_fitnessfx_v4.py		density_plot_separate_replicates_fitnessfx_v4.py
dose_response_plot.py		dose_response_plot.py
dxy_1011_naspar_44goi.py		dxy_1011_naspar_44goi.py
dyad_fraction_plot.py		dyad_fraction_plot.py

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