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alphafold

Open source code for AlphaFold.

alphalink

AlphaLink: Integrating crosslinking-MS data into OpenFold

bibliospec-docker

Create a docker image containing bibliospec executables.

biogpt

comet

An tandem mass spectrometry (MS/MS) sequence database search tool.

compare-magnum-versions-notebook

Jupyter notebook to compare Magnum versions

conga

Implementation of the CONGA algorithm for a combined open and narrow search between experimental spectra and a peptide database.

crux-toolkit

ddamsproteomics

A Nextflow MS DDA proteomics pipeline

diann-docker

Create a docker image for DIA-NN

encyclopedia-docker

A Docker build for Encyclopedia for maximum compatibility with Nextflow and AWS

fasta-profiler

Parse FASTA and output some characteristics of it.

filter-nr-fasta

Filter the nr FASTA file on any arbitrary taxonomic level and by source database

image-morphing

Implementation of image morphing

kronik

Utility for processing Hardklor features to find candidate peptides by chromatographic profiling

lorikeet

Lorikeet is a JQuery plugin to view MS/MS spectra annotated with fragment ions.

matrix-matched_calcurves

mokapot

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

mriffle

Config files for my GitHub profile.

ms-denovo-db-utils

nf-dda-tpp

Nextflow workflow for the TPP DDA pipeline

nf-dia-umpire-tpp

nf-encyclopedia

A NextFlow pipeline for chromatogram library DIA proteomics workflows

nf-filter-fasta

Nextflow workflow for creating a small FASTA from a large FASTA based on hits found by comet

nf-ms-denovo-db

nf-openmod-dda

A Nextflow workflow for open mod DDA searches

nf-skyline-targeted-import

Nextflow for import of spectra of known/expected peptides from RAW files into a Skyline document

nf-teirex-dda

nf-teirex-dia

node-trimmer

Trim a GO DAG and return leaf nodes that pass a threshold