PfTPN

This repository is to show all the analysis of the essential genome of Plasmodium falciparum via transposon mutagenesis

Name		Name	Last commit message	Last commit date
120725		120725
API_PfTPN		API_PfTPN
Essentiality_scores		Essentiality_scores
Figures		Figures
ONT_gDNA_longread		ONT_gDNA_longread
py_code		py_code
.gitignore		.gitignore
IIE_PfPkcomparison.R		IIE_PfPkcomparison.R
Insertions_distribution.R		Insertions_distribution.R
MIS_WT_vesus_MIS_MEV.R		MIS_WT_vesus_MIS_MEV.R
PfTPN_Proportion_statistics.R		PfTPN_Proportion_statistics.R
Pf_theo_TTAA_identification.R		Pf_theo_TTAA_identification.R
PlasmoDB_track.R		PlasmoDB_track.R
QC_Upset20241011.R		QC_Upset20241011.R
QC_background_genes_99CDS_sites.R		QC_background_genes_99CDS_sites.R
README.md		README.md
Step1_cm_merge_cm_Location_conversion_for_exon_or_both_exon_intron.R		Step1_cm_merge_cm_Location_conversion_for_exon_or_both_exon_intron.R
Step2_countmatrix_siteslevel_bg_noise_removal_CPM.R		Step2_countmatrix_siteslevel_bg_noise_removal_CPM.R
Step2_countmatrix_template_UTR_annotation.R		Step2_countmatrix_template_UTR_annotation.R
Step2_countmatrix_template_UTR_mcs_120225.R		Step2_countmatrix_template_UTR_mcs_120225.R
Step3_Countmatrix2transposonmatrix.R		Step3_Countmatrix2transposonmatrix.R
TTAA_bed_stats_kz.R		TTAA_bed_stats_kz.R
after_count_theo_reads_count_matrix_Pf_chimera.R		after_count_theo_reads_count_matrix_Pf_chimera.R
countmatrix_template_generation_PfTNSeq202410_chimera.R		countmatrix_template_generation_PfTNSeq202410_chimera.R
exon_intron_Description_of_data.R		exon_intron_Description_of_data.R
exploratory_qc_background_v1.R		exploratory_qc_background_v1.R
exploratory_v2.R		exploratory_v2.R
gene_stats_len_ttaa.R		gene_stats_len_ttaa.R
gene_stats_len_ttaa_1225_mcs.R		gene_stats_len_ttaa_1225_mcs.R
geneconfidentcall.R		geneconfidentcall.R
parse_sample_names.R		parse_sample_names.R
readme.txt		readme.txt
readme202504.txt		readme202504.txt
sample_variance_checking_normalization.R		sample_variance_checking_normalization.R
saturation_level_estimation_bidirectional.R		saturation_level_estimation_bidirectional.R
saturation_level_estimation_unidirectional.R		saturation_level_estimation_unidirectional.R
site_level_simulation.R		site_level_simulation.R

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