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alphapeptdeep

Deep learning framework for proteomics

alpharaw

An open-source Python package to unify raw MS data accession and storage.

batchcorrmetabolomics

Supplementary material for the paper "Improved batch correction in untargeted MS-based metabolomics" by R. Wehrens, et al. To appear in Metabolomics, 2016.

biovec

A new approach for representing biological sequences

colabfold

Making Protein folding accessible to all via Google Colab!

compomics-utilities

Open source Java library for computational proteomics

customprodbj

Customized protein database construction

deep-learning

Repo for the Deep Learning Nanodegree Foundations program.

deepdia

Using deep learning to generate in silico spectral libraries for data-independent acquisition analysis.

deeplc

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

deeplfq

deepphos

deviumweb

epept

Automatically exported from code.google.com/p/epept

ggpubr

'ggplot2' Based Publication Ready Plots

ipeak

iquant

IQuant: An automated pipeline for quantitative proteomics based upon isobaric tags

isobar

isobar - R library for the Analysis and quantitation of isobarically tagged MSMS proteomics data

java8-cheatsheet

Java 8 - Cheat Sheet

kbet

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

metabonormalyzer

metax

metaX: a flexible and comprehensive software for processing omics data.

metmsline

R functions for automation of biomarker discovery based on processing downstream of large LC-MS datasets from any peak picking software

moff

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file

msdk

MSDK source code repository

msreduce

source code for MSREDUCE

msstats

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/MSstats.html Contributions: http://msstats.org. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=MSstats or https://groups.google.com/forum/#!forum/msstats.

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

mzidlib

MzidLib - A library of routines for manipulating data in the PSI's mzIdentML standard. ProteoAnnotator is a completely automated software pipeline for integration of mass spectrometry (MS) based proteomic evidence into genome databases.