Files in ruidlpm/pathPhynder
A workflow for integrating ancient lineages into present-day Y-chromosome phylogenies.

.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/Ympute.R R/addAncToTree.R R/ancient_SNPs_to_branches.R R/assign_noNA.R R/chooseBestPath.R R/functions_pathPhynder.R R/pileup_and_filter.R README.md
data/reference_sequences/GRCH38.p12_Y.fa.gz
data/reference_sequences/GRCH38.p12_Y.fa.gz.fai
data/reference_sequences/GRCH38.p12_Y.fa.gz.gzi
data/reference_sequences/hg19_chrY.fa.gz
data/reference_sequences/hg19_chrY.fa.gz.fai
data/reference_sequences/hg19_chrY.fa.gz.gzi
data/reference_sequences/hs37d5_Y.fa.fai
data/reference_sequences/hs37d5_Y.fa.gz
data/reference_sequences/hs37d5_Y.fa.gz.fai
data/reference_sequences/hs37d5_Y.fa.gz.gzi
data/snps_isogg2018_fixed.txt
examples/imputation/fix_tree_labels.R examples/imputation/get_acc.R examples/imputation/plot_tree.R
examples/imputation/report2.txt
examples/imputation/run_analysis.sh
examples/imputation/simulate_data.py
examples/imputation/simulate_missing.R
examples/imputation/simulated_data.miss0.1.imputed.vcf
examples/imputation/simulated_data.miss0.1.vcf
examples/imputation/simulated_data.nwk
examples/imputation/simulated_data.pdf
examples/imputation/simulated_data.vcf
examples/imputation/tree_data/test.ancpos.RData
examples/imputation/tree_data/test.ancpos.txt
examples/imputation/tree_data/test.derpos.RData
examples/imputation/tree_data/test.derpos.txt
examples/imputation/tree_data/test.edge_df.txt
examples/imputation/tree_data/test.sites.bed
examples/imputation/tree_data/test.sites.txt
examples/imputation/tree_data/test.siteschr.bed
examples/snp_assignment/README.md examples/snp_assignment/plot_res.R
examples/snp_assignment/run_example.sh
examples/snp_assignment/small_example.vcf
examples/snp_assignment/small_example_tree.nwk
examples/snp_assignment/small_example_tree.pdf
examples/snp_assignment/tree_data/small_example.ancpos.RData
examples/snp_assignment/tree_data/small_example.ancpos.txt
examples/snp_assignment/tree_data/small_example.derpos.RData
examples/snp_assignment/tree_data/small_example.derpos.txt
examples/snp_assignment/tree_data/small_example.edge_df.txt
examples/snp_assignment/tree_data/small_example.report_not_added_SNPs.txt
examples/snp_assignment/tree_data/small_example.sites.bed
examples/snp_assignment/tree_data/small_example.sites.txt
examples/snp_assignment/tree_data/small_example.siteschr.bed
figures/workflow.pdf
figures/workflow.png
inst/python/call_bases_chrY_v2.1.py
pathPhynder.R tutorial/README.md
tutorial/example_problematic.png
tutorial/example_problematic_solved.png
tutorial/karmin.nwk
tutorial/karmin_hgs.txt
tutorial/sample.list
tutorial/tutorial_results.png
ruidlpm/pathPhynder documentation built on June 15, 2019, 4:49 p.m.