TF Knockdown Scripts

This repository contains all the scripts required to repeat the analysis from Cusanovich et al. 2013.

Assuming that all the appropriate annotation files have been generated, here is the order of analysis scripts:

Script Order

analysis_allthreeruv2.R
analysis_analyzer.sh (calls analysis_KdLRTRUV2_AverageNS.R)
analysis_ResultsSummary.R
combined_combining.py
combined_resultsbed2factormatrix.py
combined_PhiTables.R
combined_factormatrix2results.R
combined_annotator.R
combined_venns.R
combined_EffectSizes.R
genome_phastcons_windows.sh (calls midpoints.py)
genome_greping.py
genome_annot_overlaps.R
chromatin_bed_converter.py
chromatin_resultsbed2factormatrix.py
chromatin_factormatrix2results.R

Name		Name	Last commit message	Last commit date
Latest commit History 31 Commits
.gitignore		.gitignore
README.md		README.md
analysis_ComparePs.R		analysis_ComparePs.R
analysis_EffectSizes.R		analysis_EffectSizes.R
analysis_HT12genes.R		analysis_HT12genes.R
analysis_KdLRTRUV2_AverageNS.R		analysis_KdLRTRUV2_AverageNS.R
analysis_QCplots.R		analysis_QCplots.R
analysis_ResultsSummary.R		analysis_ResultsSummary.R
analysis_allthreeruv2.R		analysis_allthreeruv2.R
analysis_analyzer.sh		analysis_analyzer.sh
analysis_geo.R		analysis_geo.R
analysis_mavanalyzer.sh		analysis_mavanalyzer.sh
analysis_oneprobefilter.py		analysis_oneprobefilter.py
analysis_pcas_diffk.R		analysis_pcas_diffk.R
analysis_pub_mavolcanoes.R		analysis_pub_mavolcanoes.R
centipede_cagescore_sorter.py		centipede_cagescore_sorter.py
chromatin_bed_converter.py		chromatin_bed_converter.py
chromatin_factormatrix2results.R		chromatin_factormatrix2results.R
chromatin_resultsbed2factormatrix.py		chromatin_resultsbed2factormatrix.py
combined_EffectSizes.R		combined_EffectSizes.R
combined_LookingForDEOverlap.R		combined_LookingForDEOverlap.R
combined_PhiTables.R		combined_PhiTables.R
combined_annotator.R		combined_annotator.R
combined_binding_summary.R		combined_binding_summary.R
combined_bindingandDE_spearman.R		combined_bindingandDE_spearman.R
combined_causalmatrix.R		combined_causalmatrix.R
combined_combining.py		combined_combining.py
combined_factormatrix2results.R		combined_factormatrix2results.R
combined_inferring_repression.R		combined_inferring_repression.R
combined_resultsbed2factormatrix.py		combined_resultsbed2factormatrix.py
combined_subTSSdist.R		combined_subTSSdist.R
combined_tableS2.R		combined_tableS2.R
combined_venns.R		combined_venns.R
config.R		config.R
encode_uniformbedcombiner.py		encode_uniformbedcombiner.py
enhancer_factormatrix2results.R		enhancer_factormatrix2results.R
eqtls_adaptive_batcher.sh		eqtls_adaptive_batcher.sh
eqtls_alt_batcher.sh		eqtls_alt_batcher.sh
eqtls_alt_eqtlqqs.R		eqtls_alt_eqtlqqs.R
eqtls_alt_gemma_sidney.py		eqtls_alt_gemma_sidney.py
eqtls_alt_geno_collector.py		eqtls_alt_geno_collector.py
eqtls_annotator.R		eqtls_annotator.R
eqtls_batcher.sh		eqtls_batcher.sh
eqtls_eqtlqqs.R		eqtls_eqtlqqs.R
eqtls_gemma.py		eqtls_gemma.py
eqtls_gemma_sidney.py		eqtls_gemma_sidney.py
eqtls_gemma_sidney_adaptive.py		eqtls_gemma_sidney_adaptive.py
eqtls_geno_collector.py		eqtls_geno_collector.py
eqtls_qqnorm.R		eqtls_qqnorm.R
forxiang.py		forxiang.py
genome_Pritchard_eqtl_bed_filter.py		genome_Pritchard_eqtl_bed_filter.py
genome_annot_overlaps.R		genome_annot_overlaps.R
genome_dsqtlcleaner.py		genome_dsqtlcleaner.py
genome_gff2bed.py		genome_gff2bed.py
genome_greping.py		genome_greping.py
genome_greping_justperms.py		genome_greping_justperms.py
genome_greping_permadist.py		genome_greping_permadist.py
genome_phastcons_cat.sh		genome_phastcons_cat.sh
genome_phastcons_dumb.sh		genome_phastcons_dumb.sh
genome_phastcons_mean_dumb.sh		genome_phastcons_mean_dumb.sh
genome_phastcons_mean_lessdumb.sh		genome_phastcons_mean_lessdumb.sh
genome_phastcons_wig2bed_lessdumb.sh		genome_phastcons_wig2bed_lessdumb.sh
genome_phastcons_windows.sh		genome_phastcons_windows.sh
genome_pwm_calculator.py		genome_pwm_calculator.py
genome_qtlintersect.py		genome_qtlintersect.py
jackbed.py		jackbed.py
jackbed_justfilter.py		jackbed_justfilter.py
kdfunc.py		kdfunc.py
midpoints.py		midpoints.py
tableS4.py		tableS4.py
temper.R		temper.R
test.py		test.py

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