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    47 repositories

    • SeekDeep

      Public
      Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab
      bioinformaticssequence-clusteringc-plus-plus
      C++
      •
      GNU Lesser General Public License v3.0
      •5•13•7•0•Updated Dec 18, 2024Dec 18, 2024

    • MIPTools

      Public
      A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
      Jupyter Notebook
      •
      MIT License
      •9•6•12•3•Updated Dec 17, 2024Dec 17, 2024

    • seekdeep_illumina_snakemake

      Public
      a basic workflow for running seekdeep pipelines in snakemake
      Python
      •0•1•1•0•Updated Dec 9, 2024Dec 9, 2024

    • snakemake_R_maps

      Public
      a snakemake repo for mapping regional mutations in R
      R
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • labman_scripts

      Public
      growing set of utility scrips supporting lab work in the bailey lab
      Python
      •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • MIPWrangler

      Public
      Bioinformatics tools to analyze molecular inversion probe (MIP) sequencing results
      C++
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Nov 12, 2024Nov 12, 2024

    • miplicorn

      Public
      A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
      ampliconmipr
      R
      •
      Other
      •2•3•5•2•Updated Nov 4, 2024Nov 4, 2024

    • Po_popgen_snakemake

      Public
      Python
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • pfsmarrt_cameroon_7-6-24

      Public
      these are scripts used to analyze pfsmarrt amplicon performance on control datasets and 100 samples from dschang_cameroon
      Python
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • merge_probe_sets

      Public
      merges probe sets of several project resources to create a new project_resources directory
      Python
      •0•0•1•0•Updated Sep 28, 2024Sep 28, 2024

    • MSMT_2021_DR_analyses

      Public
      Python
      •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

    • seekdeep_analysis_snakemake

      Public
      Analyzes seekdeep data for read counts of individual samples
      Python
      •0•1•0•0•Updated Sep 7, 2024Sep 7, 2024

    • seekdeep_nanopore_snakemake

      Public
      a basic workflow for running seekdeep on nanopore
      Python
      •0•1•1•0•Updated Aug 5, 2024Aug 5, 2024

    • Repo_Template

      Public template
      A template for organizing and performing analysis (adapted from https://github.com/PhanstielLab/project-template).
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • selmar

      Public
      Analysis of selection coefficients for antimalarial resistance
      R
      •
      Other
      •0•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • coatswga

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • BL-Survival-Prediction-and-Prognostic-Subgrouping

      Public
      Shell
      •0•0•0•0•Updated May 2, 2024May 2, 2024

    • EBV-SWGA

      Public
      Python
      •0•0•0•0•Updated Apr 28, 2024Apr 28, 2024

    • compilerProfiler

      Public
      C++ library with an aligner to test different compiler speeds with different optimizations
      C++
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Apr 21, 2024Apr 21, 2024

    • nano_mamp_pipes

      Public
      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.
      Shell
      •0•0•0•0•Updated Mar 24, 2024Mar 24, 2024

    • miplithon

      Public
      for messing around with python/snakemake implementations of miplicorn types of functions
      Python
      •0•0•0•0•Updated Jan 20, 2024Jan 20, 2024

    • map_mip_arms

      Public
      maps the arms of a mip panel to a genome
      Python
      •0•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • merge_samplesheets

      Public
      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.
      Python
      •0•0•0•0•Updated Dec 20, 2023Dec 20, 2023

    • miptools_analysis_no_jupyter

      Public
      This is a snakemake pipeline to run miptools analysis without jupyter. It's based off of Ozkan's analysis_template_with_qual.ipynb
      Python
      •0•0•0•0•Updated Dec 1, 2023Dec 1, 2023

    • map_nonref_SNPs

      Public
      Python
      •0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • wrangler_by_sample

      Public
      runs individual samples through miptools wrangler as independent job submissions before final population-wide analysis
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Oct 26, 2023Oct 26, 2023

    • automated_demultiplexing

      Public
      automates the process of demultiplexing illumina runs
      Python
      •0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • count_undetermined_sample_barcodes

      Public
      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.
      Python
      •0•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • wrangler_snakemake

      Public
      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
      Python
      •0•0•0•0•Updated Aug 24, 2023Aug 24, 2023

    • seekdeep_vs_bwa

      Public
      snakemake pipeline for comparing observed extracted seekdeep reads against expected reads as judged by bwa
      Python
      •0•0•0•0•Updated Jun 7, 2023Jun 7, 2023