wfondrie

mokapot

Fast and flexible semi-supervised learning for peptide detection in Python

depthcharge

A deep learning toolkit for mass spectrometry

asms-ml-short-course

Links and meterials for the ASMS machine learning short course.

2024_depthcharge-demos

Demos to accompany our depthcharge manuscript

ppx

A Python interface to proteomics data repositories

ushupo-ml-short-course

Lab excerises for the introduction to ML short course at the US Hupo annual conference.

personal-website

My personal website

hugo-marmot

A minimalist, monospace Hugo theme.

2023_advent-of-code

My solutions for AoC 2023.

cv

The source for my CV and Biosketch

polars

Fast multi-threaded, hybrid-out-of-core query engine focussing on DataFrame front-ends

bioconda-recipes

Conda recipes for the bioconda channel.

2023_asms-depthcharge

Notebooks to accompany my ASMS poster on Depthcharge

ms2ml

Helps you convert raw mass spec data into tensors!

mzsniffer

Detect polymer contaminants in mass spectra.

count-org-loc

Count total lines of code across a GitHub organization

redun

Yet another redundant workflow engine

crux-toolkit

sage

Proteomics searching so fast it feels like magic

cookiecutter-python-package

A template for new Python packages

comet-mokapot-flashflq_example

An example of using Comet + Mokapot + FlashLFQ to analyze DDA proteomics data.

conda-forge-pinning-feedstock

A conda-smithy repository for conda-forge-pinning.

cloudpathlib-feedstock

A conda-smithy repository for cloudpathlib.

rich-click

Format click help output nicely with rich.

amazon-genomics-cli

msstats-demo

A demonstration of using MSstats in Python

recluse

A modification of the Hugo theme, Hermit

meth-modifications

XML-based Method Modifications

Comet

snakemake-beer-proteomics

A Snakemake tutorial workflow using the recent ABRF beer proteomics study.