Michael Riffle's repositories
nf-skyline-dia-ms
Nextflow workflow for performing DIA proteomics
nf-openmod-dda
A Nextflow workflow for open mod DDA searches
bibliospec-docker
Create a docker image containing bibliospec executables.
carafe-docker
Build a Docker image for Carafe
casanovo-docker
Build a Casanovo Docker image
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
casanovo
De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
compare-magnum-versions-notebook
Jupyter notebook to compare Magnum versions
diann-docker
Create a docker image for DIA-NN
nf-build-apptainer-images
Pre-build all apptainer images required by Nextflow workflow
nf-carafe-ai-ms
Nextflow workflow for running Carafe AI spectral library generation
nf-filter-fasta
Nextflow workflow for creating a small FASTA from a large FASTA based on hits found by comet
nf-ms-dda-casanovo
A Nextflow workflow for de novo DDA MS/MS searching using Casanovo
nf-ms-dda-tpp
Nextflow workflow for the TPP DDA pipeline
nf-skyline-targeted-import
Nextflow for import of spectra of known/expected peptides from RAW files into a Skyline document
octopus-block-randomizer
OCTOPUS - Optimized Covariate Treatment for Organized Programmatic Unified Shuffling
panorama-client-docker
Files for creating PanoramaWeb upload Docker image
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.
yarp
Yet Another Rearranger of Peptides - Generate decoy sequences from a FASTA file.