CAGE sequencing in influenza A infected human macrophages

This repository contains code for

Comprehensive characterisation of molecular host-pathogen interactions in influenza A virus-infected human macrophages

https://www.biorxiv.org/content/10.1101/670919v1

Authors: Sara Clohisey and Kenny Baillie

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
.DS_Store		.DS_Store
.gitattributes		.gitattributes
0_leader_stats.py		0_leader_stats.py
1_collate_tenmers.py		1_collate_tenmers.py
1a_chrom_locations.py		1a_chrom_locations.py
2_create_bed_file.py		2_create_bed_file.py
2a_bed_overlap_bedtools.py		2a_bed_overlap_bedtools.py
2b_create_fasta_from_bed.py		2b_create_fasta_from_bed.py
2c_leaders_alignment.sh		2c_leaders_alignment.sh
2d_cross_reference.py		2d_cross_reference.py
2e_assign_promoters_to_tenmer.py		2e_assign_promoters_to_tenmer.py
2f_collated_tenmer_promoters.py		2f_collated_tenmer_promoters.py
2g_choose_single_promoter.py		2g_choose_single_promoter.py
2h_remove_iav_from_tenmers.py		2h_remove_iav_from_tenmers.py
3a_fishers_for_summed_promoter.py		3a_fishers_for_summed_promoter.py
3b_correct_fishers.py		3b_correct_fishers.py
3c_count_multimap.py		3c_count_multimap.py
4a1_collate_pseudo.py		4a1_collate_pseudo.py
4a_fishers_for_summed_gene.py		4a_fishers_for_summed_gene.py
4a_fishers_for_summed_gene_multi.py		4a_fishers_for_summed_gene_multi.py
4b_correct_fishers.py		4b_correct_fishers.py
4c_remove_non_gene.py		4c_remove_non_gene.py
4d_choose_top_1000_by_or.py		4d_choose_top_1000_by_or.py
6a_type_rna_using_5prime_utr.py		6a_type_rna_using_5prime_utr.py
6b_type_for_boxplot_and_anova.py		6b_type_for_boxplot_and_anova.py
7a_gene_true_or_false_significant_at_previous.py		7a_gene_true_or_false_significant_at_previous.py
7b_gene_true_or_false_sigificant_at_same.py		7b_gene_true_or_false_sigificant_at_same.py
7c_count_true.py		7c_count_true.py
LICENSE		LICENSE
README.md		README.md
calculate_pvalue.py		calculate_pvalue.py
count_tenmers.py		count_tenmers.py
create_leader_table_other_datasets.py		create_leader_table_other_datasets.py
flu_prom_search.py		flu_prom_search.py
leader_search_other_datasets.py		leader_search_other_datasets.py
leader_search_pilot_genomicc.py		leader_search_pilot_genomicc.py
locate_leaders_map_filter_reduce.py		locate_leaders_map_filter_reduce.py
permute_naming.py		permute_naming.py
permute_start.py		permute_start.py
segment_counting.py		segment_counting.py
spearman_for_ranked_tenmers.py		spearman_for_ranked_tenmers.py
splice_variant.py		splice_variant.py

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saraclohisey/influenza_cage

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CAGE sequencing in influenza A infected human macrophages

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