Repositories list

• 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

  •6•16•9•0•Updated Mar 11, 2025Mar 11, 2025

• 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 Mar 3, 2025Mar 3, 2025

• MIPTools

  Public
  A suite of computational tools used for molecular inversion probe design, data processing, and analysis.

  Jupyter Notebook

  •

  MIT License

  •9•7•12•3•Updated Feb 28, 2025Feb 28, 2025

• EBV-SWGA

  Public
  Python

  •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

• haplotype_variant_calling

  Public
  uses Nick Hathaway's variantCallOnSeqAndProtein script to call variants on vcf files and generate prevalences and amino acid calls

  Python

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• seekdeep_prevalences

  Public
  converts amino acid counts files into miptools formatted counts that are suitable for prevalence estimates

  Python

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• seekdeep_illumina_snakemake

  Public
  a basic workflow for running seekdeep pipelines in snakemake

  Python

  •0•1•1•0•Updated Jan 23, 2025Jan 23, 2025

• 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

• 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

  •1•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

• 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