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modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

mscrush

mass spectrum ClusteRing Using locality Sensitive Hashing

msexample

An example R package for mass spectrometry

msfraggergo

This code does the GO analysis from the MSfragger database search results

ms_database_search

LFQ spectral clustering

nanocross

A pipeline that detect crossovers from gamete DNA of a single individual using ONT sequence libraries.

ncov

nCoV project

ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

nextflow_qc

This is a test workflow used to do the trimming and quality control of the fastq raw files

nf-core-genomeasembler

genomeasembler

nf-rnaseqcount

Assembly and differential expression analysis

nf-workflows

Repository of Nextflow+BioContainers workflows

ngs_analysis

NGS data analysis pipeline

odp

oxford dot plots

oneliners

Useful bash one-liners for bioinformatics.

paradisefish

This repository details the steps used in assembling paradise fish genome

pcatools

PCAtools: everything Principal Components Analysis

pclean

pclean_release

pClean: a tool for MS/MS spectrum preprocessing

peptide_identifcationsmethods

This repo details my chapter one of the thesis where I am looking at the different search engines and how their peptide identification rates differ and why

pga

PGA: a tool for ProteoGenomics Analysis

pgdb

The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.

phd_rcodes

This repo contains the codes used in the analysis of proteomics data for my PhD project.

plascad

Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.

platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

proteindifferentialanalysis

Label free differential analysis

proteogenomics

proteogenomics-analysis-workflow

IPAW: a Nextflow workflow for proteogenomics

proteomicslfq

UNDER CONSTRUCTION - Proteomics label-free quantification (LFQ) analysis pipeline