{"repo":"arvkevi/ezancestry","free":true,"listed":false,"github":"https://github.com/arvkevi/ezancestry","clone":"git clone https://github.com/arvkevi/ezancestry.git","description":"Easy genetic ancestry predictions in Python","language":"Jupyter Notebook","stars":70,"topics":["genomics","genomics-visualization","personal-genomics","streamlit","data-visualization","dimensionality-reduction","ancestry","genotypes"],"license":"MIT","category":"machine-learning","readme_excerpt":"ezancestry Easily visualize your direct-to-consumer genetics next to 2500+ samples from the 1000 genomes project. Evaluate the performance of a custom set of ancestry-informative snps (AISNPs) at classifying the genetic ancestry of the 1000 genomes samples using a machine learning model. A subset of 1000 Genomes Project samples' single nucleotide polymorphism(s), or, SNP(s) have been parsed from the publicly available .bcf files. The subset of SNPs , AISNPs (ancestry-informative snps), were chosen from two publications: Set of 55 AISNPs. Progress toward an efficient panel of SNPs for ancestry inference. Kidd et al. 2014 Set of 128 AISNPs. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.. Kosoy et al. 2009 (Seldin Lab) ezancestry ships with pretrained k-nearest neighbor models for all combinations of following: Kidd (55 AISNPs) Seldin (128 AISNPs) continental-level population (superpopulation) regional population (population) principal component analysis (PCA) Table of Contents Installation Config Usage command line tool fetch predict plot train Python API Visualization Contributing Installation Install ezancestry with pip: Or clone the repository and run pip install from the directory: Config The first time ezancestry is run it will generate a config.ini file and data/ directory in your home directory under ${HOME}/.ezancestry . You can edit conf.ini to change the default settings, but it is not ne","default_branch":null,"files":null,"tree":[],"storefront":"/r/arvkevi","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/arvkevi/ezancestry/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}