GitHub - BrianLohman/py_tools: Collection of in progress scripts for genomics with python

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Collection of in progress scripts for genomics with python

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Name		Name	Last commit message	Last commit date
Latest commit History 115 Commits
.pre-commit-config.yaml		.pre-commit-config.yaml
Generate_PRS_report.py		Generate_PRS_report.py
Generate_map.py		Generate_map.py
assoc-to-bed.py		assoc-to-bed.py
batch_chpc.py		batch_chpc.py
bim-to-bed.py		bim-to-bed.py
bim_chrBP_to_rsID.py		bim_chrBP_to_rsID.py
bim_rsID_2_chr-bp.py		bim_rsID_2_chr-bp.py
bins_by_mutation_load.py		bins_by_mutation_load.py
build_regions.py		build_regions.py
build_unthinned_regions.py		build_unthinned_regions.py
collect_kraken2_reports.py		collect_kraken2_reports.py
count_bases.py		count_bases.py
cpg_lookup.py		cpg_lookup.py
ct_enrichment_ttest.py		ct_enrichment_ttest.py
extract.py		extract.py
extract_gene_names_from_pathways.py		extract_gene_names_from_pathways.py
extract_hg38.py		extract_hg38.py
fast_filter_variant_table.py		fast_filter_variant_table.py
filter_readback_phasing.py		filter_readback_phasing.py
find_complex_insertion.py		find_complex_insertion.py
fix_bim_alt_ref.py		fix_bim_alt_ref.py
fix_bim_ref_alt.py		fix_bim_ref_alt.py
gwas_check.py		gwas_check.py
gwas_chrBP_2_rsID.py		gwas_chrBP_2_rsID.py
gwas_lift.py		gwas_lift.py
gwas_rsID_2_chrBP.py		gwas_rsID_2_chrBP.py
id_check.py		id_check.py
impact_table_summary.py		impact_table_summary.py
intersect_pathway_SFARI.py		intersect_pathway_SFARI.py
lift.py		lift.py
list_build_regions.py		list_build_regions.py
make_ped.py		make_ped.py
map-to-bed.py		map-to-bed.py
no_flip_lift.py		no_flip_lift.py
parse_kraken2_report.py		parse_kraken2_report.py
plot_pca_by_prs_quartile.py		plot_pca_by_prs_quartile.py
plotting_prs_statification_vs_simuated_null.py		plotting_prs_statification_vs_simuated_null.py
prs_based_go_enrichment.py		prs_based_go_enrichment.py
pysam_count_bases.py		pysam_count_bases.py
query_panther.py		query_panther.py
reduce_gene_models.py		reduce_gene_models.py
remove_regions_overlaps.py		remove_regions_overlaps.py
replicate_by_variant_count.py		replicate_by_variant_count.py
rsID_2_chr-bp.py		rsID_2_chr-bp.py
shuffle_split_test.py		shuffle_split_test.py
simons_format_to_bed.py		simons_format_to_bed.py
simulate_enrichment_null_SSC_probands.py		simulate_enrichment_null_SSC_probands.py
slow_filter_variant_table.py		slow_filter_variant_table.py
split_bed_by_chrom.py		split_bed_by_chrom.py
split_by_pathway.py		split_by_pathway.py
split_test.py		split_test.py
subset_UCSC_150_by_EUR_snps.py		subset_UCSC_150_by_EUR_snps.py
tacc_launcher_creator.py		tacc_launcher_creator.py
transcript_to_genomic_coords.py		transcript_to_genomic_coords.py
tree_build_regions.py		tree_build_regions.py