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yjx1217

better installation robustness

Feb 18, 2025

474776a · Feb 18, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
CNV_segmentation_by_DNAcopy.R		CNV_segmentation_by_DNAcopy.R	release candidate 20210310	Mar 10, 2021
adjust_FREEC_copynumber_by_DNAcopy_copynumber.pl		adjust_FREEC_copynumber_by_DNAcopy_copynumber.pl	release candidate 20210310	Mar 10, 2021
assess_CNV_significance_for_FREEC.R		assess_CNV_significance_for_FREEC.R	release candidate 20210310	Mar 10, 2021
batch_gamete_based_recombination_profiling_by_parent_genomes.pl		batch_gamete_based_recombination_profiling_by_parent_genomes.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
batch_gamete_based_recombination_profiling_by_reference_genome.pl		batch_gamete_based_recombination_profiling_by_reference_genome.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
batch_genotype_plotting_by_parent_genomes.pl		batch_genotype_plotting_by_parent_genomes.pl	release candidate 20210310	Mar 10, 2021
batch_genotype_plotting_by_reference_genome.pl		batch_genotype_plotting_by_reference_genome.pl	release candidate 20210310	Mar 10, 2021
batch_genotype_segregation_summarizing_by_parent_genomes.pl		batch_genotype_segregation_summarizing_by_parent_genomes.pl	release candidate 20210310	Mar 10, 2021
batch_genotype_segregation_summarizing_by_reference_genome.pl		batch_genotype_segregation_summarizing_by_reference_genome.pl	release candidate 20210310	Mar 10, 2021
batch_parental_allele_frequency_in_tetrads_profiling_by_parent_genomes.pl		batch_parental_allele_frequency_in_tetrads_profiling_by_parent_genomes.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
batch_parental_allele_frequency_in_tetrads_profiling_by_reference_genome.pl		batch_parental_allele_frequency_in_tetrads_profiling_by_reference_genome.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
batch_parental_allele_frequency_in_tetrads_profiling_by_reference_genome_old.pl		batch_parental_allele_frequency_in_tetrads_profiling_by_reference_genome_old.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
batch_prepare_input_for_genotype_plotting.pl		batch_prepare_input_for_genotype_plotting.pl	release candidate 20210310	Mar 10, 2021
batch_read_mapping_to_parent_genomes.pl		batch_read_mapping_to_parent_genomes.pl	various feature polishing	Jun 27, 2021
batch_read_mapping_to_reference_genome.pl		batch_read_mapping_to_reference_genome.pl	various feature polishing	Jun 27, 2021
batch_recombination_plotting_by_parent_genomes.pl		batch_recombination_plotting_by_parent_genomes.pl	release candidate 20210310	Mar 10, 2021
batch_recombination_plotting_by_reference_genome.pl		batch_recombination_plotting_by_reference_genome.pl	release candidate 20210310	Mar 10, 2021
batch_recombinex_genotype2rqtl_genotype_by_parent_genomes.pl		batch_recombinex_genotype2rqtl_genotype_by_parent_genomes.pl	release candidate 20211212	Dec 25, 2021
batch_recombinex_genotype2rqtl_genotype_by_reference_genome.pl		batch_recombinex_genotype2rqtl_genotype_by_reference_genome.pl	release candidate 20211212	Dec 25, 2021
batch_tetrad_based_recombination_profiling_by_parent_genomes.pl		batch_tetrad_based_recombination_profiling_by_parent_genomes.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
batch_tetrad_based_recombination_profiling_by_reference_genome.pl		batch_tetrad_based_recombination_profiling_by_reference_genome.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
batch_tetrad_genotyping_by_parent_genomes.pl		batch_tetrad_genotyping_by_parent_genomes.pl	release candidate 20211212	Dec 25, 2021
batch_tetrad_genotyping_by_reference_genome.pl		batch_tetrad_genotyping_by_reference_genome.pl	release candidate 20211212	Dec 25, 2021
cal_GC_range_for_FREEC.pl		cal_GC_range_for_FREEC.pl	release candidate 20210310	Mar 10, 2021
event_count_vs_chr_length.pl		event_count_vs_chr_length.pl	release candidate 20210310	Mar 10, 2021
extract_polymorphic_markers_by_reference_based_vcf.pl		extract_polymorphic_markers_by_reference_based_vcf.pl	release candidate 20210310	Mar 10, 2021
extract_syntenic_region.pl		extract_syntenic_region.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
filter_gff_by_feature.pl		filter_gff_by_feature.pl	release candidate 20210310	Mar 10, 2021
filter_markers_from_opposite_chromosome_arms.pl		filter_markers_from_opposite_chromosome_arms.pl	release candidate 20210310	Mar 10, 2021
filter_nonreciprocal_markers.pl		filter_nonreciprocal_markers.pl	release candidate 20210310	Mar 10, 2021
filter_parent_based_markers_by_mpileup_and_depth.pl		filter_parent_based_markers_by_mpileup_and_depth.pl	release_v1.0.0	May 7, 2022
filter_reference_based_markers_by_mpileup_and_depth.pl		filter_reference_based_markers_by_mpileup_and_depth.pl	release_v1.0.0	May 7, 2022
filter_vcf_by_window.pl		filter_vcf_by_window.pl	release candidate 20210310	Mar 10, 2021
find_motif_in_genome.pl		find_motif_in_genome.pl	release candidate 20210310	Mar 10, 2021
intermarker_distance.pl		intermarker_distance.pl	release candidate 20210310	Mar 10, 2021
mummer2vcf.pl		mummer2vcf.pl	release candidate 20210310	Mar 10, 2021
plot_CNV_for_FREEC.R		plot_CNV_for_FREEC.R	release candidate 20210310	Mar 10, 2021
plot_event_count_vs_chr_length.R		plot_event_count_vs_chr_length.R	release candidate 20210310	Mar 10, 2021
plot_markers.R		plot_markers.R	better installation robustness	Feb 18, 2025
plot_parental_allele_frequency_in_tetrads.R		plot_parental_allele_frequency_in_tetrads.R	manual updates and minor improvements	Apr 3, 2022
plot_recombination_frequency.R		plot_recombination_frequency.R	v1.0.0 -> v1.1.0	Aug 22, 2022
plot_tetrad_genotype.R		plot_tetrad_genotype.R	better installation robustness	Feb 18, 2025
plot_tetrad_genotype_for_simulation.R		plot_tetrad_genotype_for_simulation.R	better installation robustness	Feb 18, 2025
prepare_genome_for_FREEC.pl		prepare_genome_for_FREEC.pl	release candidate 20210310	Mar 10, 2021
profile_GC_sliding_window.pl		profile_GC_sliding_window.pl	release candidate 20210310	Mar 10, 2021
profile_marker_density_sliding_window.pl		profile_marker_density_sliding_window.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
profile_masking_sliding_window.pl		profile_masking_sliding_window.pl	release candidate 20210310	Mar 10, 2021
profile_recombination_event_count.pl		profile_recombination_event_count.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
profile_recombination_frequency.pl		profile_recombination_frequency.pl	v1.0.0 -> v1.1.0	Aug 22, 2022
relabel_chr_in_gff.pl		relabel_chr_in_gff.pl	release candidate 20210310	Mar 10, 2021
run_FREEC_wrapper.pl		run_FREEC_wrapper.pl	Update run_FREEC_wrapper.pl	Apr 12, 2023
run_FREEC_wrapper_lite.pl		run_FREEC_wrapper_lite.pl	release candidate 20210310	Mar 10, 2021
run_FREEC_wrapper_lite_for_RecombineX.pl		run_FREEC_wrapper_lite_for_RecombineX.pl	release candidate 20210310	Mar 10, 2021
run_prepare_LiftOver_chain.sh		run_prepare_LiftOver_chain.sh	release candidate 20210310	Mar 10, 2021
run_profiling_parental_allele_frequency.sh		run_profiling_parental_allele_frequency.sh	release candidate 20210310	Mar 10, 2021
select_fasta_by_list.pl		select_fasta_by_list.pl	release candidate 20210310	Mar 10, 2021
select_sequences_by_list.pl		select_sequences_by_list.pl	release candidate 20210310	Mar 10, 2021
simulate_recombinant_tetrad.pl		simulate_recombinant_tetrad.pl	release candidate 20210310	Mar 10, 2021
softmask2hardmask.pl		softmask2hardmask.pl	release candidate 20210310	Mar 10, 2021
summarize_mapping_coverage.pl		summarize_mapping_coverage.pl	release candidate 20210310	Mar 10, 2021
summarize_mapping_coverage_adv.pl		summarize_mapping_coverage_adv.pl	release candidate 20210310	Mar 10, 2021
switch_letter_cases_in_fasta.pl		switch_letter_cases_in_fasta.pl	release candidate 20210310	Mar 10, 2021
tidy_SGDref_genome.pl		tidy_SGDref_genome.pl	release candidate 20210310	Mar 10, 2021
tidy_fasta.pl		tidy_fasta.pl	release candidate 20210310	Mar 10, 2021
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