Michael Riffle's repositories
nf-openmod-dda
A Nextflow workflow for open mod DDA searches
alphafold
Open source code for AlphaFold.
AlphaLink
AlphaLink: Integrating crosslinking-MS data into OpenFold
bibliospec-docker
Create a docker image containing bibliospec executables.
Comet
An tandem mass spectrometry (MS/MS) sequence database search tool.
CONGA
Implementation of the CONGA algorithm for a combined open and narrow search between experimental spectra and a peptide database.
encyclopedia-docker
A Docker build for Encyclopedia for maximum compatibility with Nextflow and AWS
fasta-profiler
Parse FASTA and output some characteristics of it.
compare-magnum-versions-notebook
Jupyter notebook to compare Magnum versions
diann-docker
Create a docker image for DIA-NN
nf-dda-tpp
Nextflow workflow for the TPP DDA pipeline
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-skyline-targeted-import
Nextflow for import of spectra of known/expected peptides from RAW files into a Skyline document
node-trimmer
Trim a GO DAG and return leaf nodes that pass a threshold
octopus-block-randomizer
OCTOPUS - Optimized Covariate Treatment for Organized Programmatic Unified Shuffling
panorama-client-docker
Files for creating PanoramaWeb upload Docker image
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
sphinx-readthedocs
Docker image for building and testing RST documentation destined for readthedocs
teirex-aws-setup
Source code for documentation for setting up AWS for TEI-REX Nextflow workflows.