Bo's repositories
Customprodbj
Customized protein database construction
alphapeptdeep
Deep learning framework for proteomics
alpharaw
An open-source Python package to unify raw MS data accession and storage.
ColabFold
Making Protein folding accessible to all via Google Colab!
compomics-utilities
Open source Java library for computational proteomics
DeepLC
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
ggpubr
'ggplot2' Based Publication Ready Plots
isobar
isobar - R library for the Analysis and quantitation of isobarically tagged MSMS proteomics data
kBET
An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
moFF
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
MusiteDeep
MusiteDeep provides a deep-learning method for general and kinase-specific phosphorylation site prediction. It is implemented by deep learning library Keras and Theano backend (the Keras2.0 and Tensorflow backend were also provided under folder MusiteDeep_Keras2.0). At present, MusiteDeep only provides prediction of human phosphorylation sites; however, it also provides customized model training that enables users to train other PTM prediction models by using their own training data sets based on either CPU or GPU.
MusiteDeep_web
This repository contains the stand-alone tool for MusiteDeep server
pDeep
pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning
prosit
Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7