{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"MIPTools","owner":"bailey-lab","isFork":false,"description":"A suite of computational tools used for molecular inversion probe design, data processing, and analysis.","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":3,"issueCount":12,"starsCount":6,"forksCount":9,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-08T18:34:48.260Z"}},{"type":"Public","name":"pfsmarrt_cameroon_7-6-24","owner":"bailey-lab","isFork":false,"description":"these are scripts used to analyze pfsmarrt amplicon performance on control datasets and 100 samples from dschang_cameroon","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-06T18:31:59.561Z"}},{"type":"Public","name":"SeekDeep","owner":"bailey-lab","isFork":false,"description":"Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab","allTopics":["bioinformatics","sequence-clustering","c-plus-plus"],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":7,"starsCount":13,"forksCount":5,"license":"GNU Lesser General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-02T04:37:07.817Z"}},{"type":"Public","name":"Po_popgen_snakemake","owner":"bailey-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-14T18:30:57.179Z"}},{"type":"Public","name":"seekdeep_nanopore_snakemake","owner":"bailey-lab","isFork":false,"description":"a basic workflow for running seekdeep on nanopore","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-11T15:45:27.636Z"}},{"type":"Public","name":"selmar","owner":"bailey-lab","isFork":false,"description":"Analysis of selection coefficients for antimalarial resistance","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-07T19:59:57.420Z"}},{"type":"Public","name":"coatswga","owner":"bailey-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":[10,14,8,3,13,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,1,2,0,0,3,0,0,7,1,0,8,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-07T18:17:03.279Z"}},{"type":"Public","name":"seekdeep_analysis_snakemake","owner":"bailey-lab","isFork":false,"description":"Analyzes seekdeep data for read counts of individual samples","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,2,0,2,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-09T12:01:46.186Z"}},{"type":"Public","name":"BL-Survival-Prediction-and-Prognostic-Subgrouping","owner":"bailey-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-02T02:55:32.973Z"}},{"type":"Public","name":"seekdeep_illumina_snakemake","owner":"bailey-lab","isFork":false,"description":"a basic workflow for running seekdeep pipelines in snakemake","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-29T09:26:49.611Z"}},{"type":"Public","name":"EBV-SWGA","owner":"bailey-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-28T20:43:53.897Z"}},{"type":"Public","name":"MIPWrangler","owner":"bailey-lab","isFork":false,"description":"Bioinformatics tools to analyze molecular inversion probe (MIP) sequencing results ","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-21T20:01:20.788Z"}},{"type":"Public","name":"compilerProfiler","owner":"bailey-lab","isFork":false,"description":"C++ library with an aligner to test different compiler speeds with different optimizations","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"GNU General Public License v2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-21T20:01:14.144Z"}},{"type":"Public","name":"miplicorn","owner":"bailey-lab","isFork":false,"description":"A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.","allTopics":["amplicon","mip","r"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":2,"issueCount":5,"starsCount":3,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-15T22:14:26.495Z"}},{"type":"Public","name":"MSMT_2021_DR_analyses","owner":"bailey-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-28T21:10:17.222Z"}},{"type":"Public","name":"nano_mamp_pipes","owner":"bailey-lab","isFork":false,"description":"NanoMAMP Pipes is a free-to-use one-step automated pipeline designed for comprehensive analysis of molecular inversion probe and amplicon sequencing data from Nanopore platforms.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-24T19:59:13.412Z"}},{"type":"Public","name":"miplithon","owner":"bailey-lab","isFork":false,"description":"for messing around with python/snakemake implementations of miplicorn types of functions","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-20T15:53:40.310Z"}},{"type":"Public","name":"map_mip_arms","owner":"bailey-lab","isFork":false,"description":"maps the arms of a mip panel to a genome","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-17T17:14:20.670Z"}},{"type":"Public","name":"merge_samplesheets","owner":"bailey-lab","isFork":false,"description":"this is a wrapper for Jeff's program that merges samplesheets. Written to allow an easy record of settings used to produce each merged sample sheet.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-20T23:10:17.863Z"}},{"type":"Public","name":"miptools_analysis_no_jupyter","owner":"bailey-lab","isFork":false,"description":"This is a snakemake pipeline to run miptools analysis without jupyter. It's based off of Ozkan's analysis_template_with_qual.ipynb","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-01T17:00:48.968Z"}},{"type":"Public","name":"map_nonref_SNPs","owner":"bailey-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-31T22:51:00.104Z"}},{"type":"Public","name":"wrangler_by_sample","owner":"bailey-lab","isFork":false,"description":"runs individual samples through miptools wrangler as independent job submissions before final population-wide analysis","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-26T17:13:22.491Z"}},{"type":"Public","name":"merge_probe_sets","owner":"bailey-lab","isFork":false,"description":"merges probe sets of several project resources to create a new project_resources directory","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-05T18:48:21.226Z"}},{"type":"Public","name":"automated_demultiplexing","owner":"bailey-lab","isFork":false,"description":"automates the process of demultiplexing illumina runs","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-27T16:03:47.439Z"}},{"type":"Public","name":"count_undetermined_sample_barcodes","owner":"bailey-lab","isFork":false,"description":"when demultiplexing fails, we need the ability to figure out which sample barcodes were present and in what abundances. This allows us to figure out if the 'wrong' barcodes were applied to the samples or if the barcoding failed.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-31T19:26:15.408Z"}},{"type":"Public","name":"wrangler_snakemake","owner":"bailey-lab","isFork":false,"description":"this is a re-implementation of the miptools wrangler singularity app, but with Nick's component C++ programs split out into separate rules for benchmarking","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-24T19:36:41.730Z"}},{"type":"Public","name":"seekdeep_vs_bwa","owner":"bailey-lab","isFork":false,"description":"snakemake pipeline for comparing observed extracted seekdeep reads against expected reads as judged by bwa","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-07T21:15:01.097Z"}},{"type":"Public","name":"coiaf-manuscript-work","owner":"bailey-lab","isFork":false,"description":"Code and figures for the coiaf publication","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-13T02:48:04.403Z"}},{"type":"Public","name":"map_fastqs_snakemake","owner":"bailey-lab","isFork":false,"description":"a snakemake pipeline for mapping fastq entries to a bowtie2 indexed reference genome","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-30T22:43:53.644Z"}},{"type":"Public","name":"coiaf","owner":"bailey-lab","isFork":false,"description":"Complexity of Infection Estimation with Allele Frequencies","allTopics":["estimation","coi","allele-frequencies","complexity-of-infection"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":3,"starsCount":3,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-14T03:01:31.289Z"}}],"repositoryCount":45,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"bailey-lab repositories"}