Pinned Repositories
cptac-annotare
annotare for cptac raw data
MathModel
研究生数学建模，本科生数学建模、数学建模竞赛优秀论文，数学建模算法，LaTeX论文模板，算法思维导图，参考书籍，Matlab软件教程，PPT
proteomics-metadata-standard
The Proteomics Experimental Design file format: Standard for experimental design annotation
proteomics-tutorial
proteomicslfq
UNDER CONSTRUCTION - Proteomics label-free quantification (LFQ) analysis pipeline
ProteomicsVisualization
This is a collection of minimal code to visualize various aspects of proteomics data.
Python
My Python Examples
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
quantms-research
This repository contains a set of JupyterNotebooks and code with analysis and plots for the pipeline https://github.com/bigbio/quantms
sdrf-pipelines
A repository to convert SDRF proteomics files into pipelines config files
daichengxin's Repositories
daichengxin/quantms-research
This repository contains a set of JupyterNotebooks and code with analysis and plots for the pipeline https://github.com/bigbio/quantms
daichengxin/proteomics-metadata-standard
The Proteomics Experimental Design file format: Standard for experimental design annotation
daichengxin/quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
daichengxin/quantms-utils
A python library with scripts and helpers classes for quantms workflow
daichengxin/sdrf-pipelines
A repository to convert SDRF proteomics files into pipelines config files
daichengxin/alphadia
modular & open DIA search
daichengxin/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
daichengxin/CLIP
CLIP (Contrastive Language-Image Pretraining), Predict the most relevant text snippet given an image
daichengxin/glycowork
Package for processing and analyzing glycans and their role in biology.
daichengxin/glycresoft
An LC-MS/MS glycan and glycopeptide search engine
daichengxin/glypy
Glycan Analysis and Glycoinformatics Library for Python
daichengxin/ibaqpy
Trying out some ibaq code with pyopenms
daichengxin/LSD
:exclamation: This is a read-only mirror of the CRAN R package repository. LSD — Lots of Superior Depictions
daichengxin/mad_decoy
Mad decoy is a decoy simulation tool to assess large-scale merge of q-values.
daichengxin/MetaMorpheus
Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
daichengxin/MSnet
A large open benchmark dataset for computational proteomics
daichengxin/multiomics-configs
Set of config files for species, taxonomies, etc
daichengxin/mztabpy
Python library to handle mzTab files
daichengxin/os-proteomics
View point in Open source in Proteomics
daichengxin/pmultiqc
A library for QC report based on MultiQC framework
daichengxin/pridepy
Python client for PRIDE Archive Rest API.
daichengxin/proteomics-quant-formats
The proteomics quantification format, extending mzTab for large scale datasets.
daichengxin/ProteomicsML
Community-curated tutorials and datasets for ML in proteomics
daichengxin/pyCircos
python Circos
daichengxin/quantms-rescoring
quantms and ms2rescore helper functions and scripts
daichengxin/quantms.io
The proteomics quantification format, extending mzTab for large scale datasets.
daichengxin/quantms.org
Web page storing all the datasets renalyzed with quantms
daichengxin/sdrf-utils
sdrf-cls
daichengxin/test-datasets
Test data to be used for automated testing with the nf-core pipelines
daichengxin/timsconvert