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.gitignore
.gitignore
 
 
0.1.hist_fragment_size.R
0.1.hist_fragment_size.R
 
 
1.QC.Rmd
1.QC.Rmd
 
 
1.QC.html
1.QC.html
 
 
2.Differential_ATAC-seq_analysis_all.Rmd
2.Differential_ATAC-seq_analysis_all.Rmd
 
 
2.Differential_ATAC-seq_analysis_all.html
2.Differential_ATAC-seq_analysis_all.html
 
 
3.1.1. WGCNA_modules_mean_range.R
3.1.1. WGCNA_modules_mean_range.R
 
 
3.1.filter_WGCNA_modules_by_MM.R
3.1.filter_WGCNA_modules_by_MM.R
 
 
3.2.WGCNA_modules_to_fGWAS_input.R
3.2.WGCNA_modules_to_fGWAS_input.R
 
 
3.3.make_peak_file_WGCNA_input_HOMER.R
3.3.make_peak_file_WGCNA_input_HOMER.R
 
 
3.5.check_file_motifs_locations_in_peaks.R
3.5.check_file_motifs_locations_in_peaks.R
 
 
3.5.combineMotifs.sh
3.5.combineMotifs.sh
 
 
3.6.WGCNA_HOMER_overlap_credset.R
3.6.WGCNA_HOMER_overlap_credset.R
 
 
3.WGCNA_clustering.R
3.WGCNA_clustering.R
 
 
Differential_ATAC-seq_analysis_reduced.R
Differential_ATAC-seq_analysis_reduced.R
 
 
Filtering_and_differential_analysis_of_peaks.R
Filtering_and_differential_analysis_of_peaks.R
 
 
LICENSE
LICENSE
 
 
PCA_from_bedgraph.R
PCA_from_bedgraph.R
 
 
QC_peaks_normalized_from_bam_no_intersect.R
QC_peaks_normalized_from_bam_no_intersect.R
 
 
README.md
README.md
 
 
SNPs_overlap_peaks.R
SNPs_overlap_peaks.R
 
 
WGCNA_HOMER_overlap_credset.R
WGCNA_HOMER_overlap_credset.R
 
 
annotate_GRanges_TxDb.R
annotate_GRanges_TxDb.R
 
 
annotate_peaks_near_genes.R
annotate_peaks_near_genes.R
 
 
annotate_whole_genome_TxDb.R
annotate_whole_genome_TxDb.R
 
 
are_seqs_in_peaks.R
are_seqs_in_peaks.R
 
 
atac-seq.Rproj
atac-seq.Rproj
 
 
corWGCNAmodules.R
corWGCNAmodules.R
 
 
corr_peak_cpms_vs_RNA_tpms.R
corr_peak_cpms_vs_RNA_tpms.R
 
 
count_coverage_peaks_file.R
count_coverage_peaks_file.R
 
 
distribution_of_reads_per_peak.Rmd
distribution_of_reads_per_peak.Rmd
 
 
edgeR_exploratory_normalization.Rmd
edgeR_exploratory_normalization.Rmd
 
 
examine_PCA_ATAC.R
examine_PCA_ATAC.R
 
 
exploratory_QC.Rmd
exploratory_QC.Rmd
 
 
merged_peaks_to_fGWAS_input.R
merged_peaks_to_fGWAS_input.R
 
 
non-promoter_plot_longitudinal_variation_peak_counts.R
non-promoter_plot_longitudinal_variation_peak_counts.R
 
 
peaksOverCredsets_cor_genes.R
peaksOverCredsets_cor_genes.R
 
 
peaks_merged_to_binary_df.R
peaks_merged_to_binary_df.R
 
 
peaks_to_genes_ChIPpeakAnno.R
peaks_to_genes_ChIPpeakAnno.R
 
 
plot_coverage.R
plot_coverage.R
 
 
plot_expression_top_peaks.Rmd
plot_expression_top_peaks.Rmd
 
 
plot_longitudinal_variation_peak_counts.R
plot_longitudinal_variation_peak_counts.R
 
 
plot_mean_ATAC_selected_stage_andSNPs.R
plot_mean_ATAC_selected_stage_andSNPs.R
 
 
plot_total_counts_vs_peak_number.R
plot_total_counts_vs_peak_number.R
 
 
promoter_plot_longitudinal_variation_peak_counts.R
promoter_plot_longitudinal_variation_peak_counts.R
 
 
rename_matrix_peak_count.R
rename_matrix_peak_count.R
 
 
sort_by_2_strings.R
sort_by_2_strings.R
 
 

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atac-seq

Analysis of atac-seq data in differentiated iPSC

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Analysis of atac-seq data in differentiated iPSC

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