Chengxin Dai's repositories
proteomics-metadata-standard
The Proteomics Experimental Design file format: Standard for experimental design annotation
quantms-research
This repository contains a set of JupyterNotebooks and code with analysis and plots for the pipeline https://github.com/bigbio/quantms
quantms-utils
A python library with scripts and helpers classes for quantms workflow
sdrf-pipelines
A repository to convert SDRF proteomics files into pipelines config files
alphadia
modular & open DIA search
CKG
Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical databases 2) automate knowledge discovery making use of all the information contained in the graph
glycowork
Package for processing and analyzing glycans and their role in biology.
glycresoft
An LC-MS/MS glycan and glycopeptide search engine
glypy
Glycan Analysis and Glycoinformatics Library for Python
ibaqpy
Trying out some ibaq code with pyopenms
LSD
:exclamation: This is a read-only mirror of the CRAN R package repository. LSD — Lots of Superior Depictions
mad_decoy
Mad decoy is a decoy simulation tool to assess large-scale merge of q-values.
MetaMorpheus
Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MSnet
A large open benchmark dataset for computational proteomics
msstitch
MS proteomics post-processing utilities
multiomics-configs
Set of config files for species, taxonomies, etc
mztabpy
Python library to handle mzTab files
pmultiqc
A library for QC report based on MultiQC framework
pridepy
Python client for PRIDE Archive Rest API.
proteomics-quant-formats
The proteomics quantification format, extending mzTab for large scale datasets.
ProteomicsML
Community-curated tutorials and datasets for ML in proteomics
pyCircos
python Circos
quantms.io
The proteomics quantification format, extending mzTab for large scale datasets.
quantms.org
Web page storing all the datasets renalyzed with quantms
sdrf-utils
sdrf-cls
test-datasets
Test data to be used for automated testing with the nf-core pipelines