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
Latest commit History 14 Commits
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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