Pinned Repositories
casanovo
De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
cookiecutter-data-science
A template for data science projects at Talus Bio
asms-ml-short-course
Links and meterials for the ASMS machine learning short course.
depthcharge
A deep learning toolkit for mass spectrometry
mokapot
Fast and flexible semi-supervised learning for peptide detection in Python
mzsniffer
Detect polymer contaminants in mass spectra.
ppx
A Python interface to proteomics data repositories
pydeck
Easy remark slide decks using Python and markdown.
recluse
A modification of the Hugo theme, Hermit
slides
My public slide decks
wfondrie's Repositories
wfondrie/depthcharge
A deep learning toolkit for mass spectrometry
wfondrie/mokapot
Fast and flexible semi-supervised learning for peptide detection in Python
wfondrie/ppx
A Python interface to proteomics data repositories
wfondrie/mzsniffer
Detect polymer contaminants in mass spectra.
wfondrie/asms-ml-short-course
Links and meterials for the ASMS machine learning short course.
wfondrie/recluse
A modification of the Hugo theme, Hermit
wfondrie/2023_asms-depthcharge
Notebooks to accompany my ASMS poster on Depthcharge
wfondrie/msstats-demo
A demonstration of using MSstats in Python
wfondrie/Comet
wfondrie/cookiecutter-python-package
A template for new Python packages
wfondrie/meth-modifications
XML-based Method Modifications
wfondrie/2024_depthcharge-demos
Demos to accompany our depthcharge manuscript
wfondrie/amazon-genomics-cli
wfondrie/bioconda-recipes
Conda recipes for the bioconda channel.
wfondrie/cloudpathlib-feedstock
A conda-smithy repository for cloudpathlib.
wfondrie/comet-mokapot-flashflq_example
An example of using Comet + Mokapot + FlashLFQ to analyze DDA proteomics data.
wfondrie/conda-forge-pinning-feedstock
A conda-smithy repository for conda-forge-pinning.
wfondrie/count-org-loc
Count total lines of code across a GitHub organization
wfondrie/crux-toolkit
wfondrie/cv
The source for my CV and Biosketch
wfondrie/hugo-marmot
A minimalist, monospace Hugo theme.
wfondrie/ms2ml
Helps you convert raw mass spec data into tensors!
wfondrie/personal-website
My personal website
wfondrie/polars
Fast multi-threaded, hybrid-out-of-core query engine focussing on DataFrame front-ends
wfondrie/redun
Yet another redundant workflow engine
wfondrie/rich-click
Format click help output nicely with rich.
wfondrie/sage
Proteomics searching so fast it feels like magic
wfondrie/snakemake-beer-proteomics
A Snakemake tutorial workflow using the recent ABRF beer proteomics study.
wfondrie/2023_advent-of-code
My solutions for AoC 2023.
wfondrie/ushupo-ml-short-course
Lab excerises for the introduction to ML short course at the US Hupo annual conference.