All Categories → No Category → proteomics

Top 24 proteomics open source projects

searchgui

Highly adaptable common interface for proteomics search and de novo engines

✭ 22

java HTML XSLT perl GDB bioinformatics proteomics protein-identification

bacnet

BACNET is a Java based platform to develop website for multi-omics analysis

✭ 12

java website bioinformatics genomics data-visualization proteomics transcriptomics bacnet multi-omics listeria

MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

✭ 43

HTML bioinformatics proteomics mass-spectrometry database-search

DAtest

Compare different differential abundance and expression methods

✭ 34

r metagenomics rnaseq auc proteomics metabolomics microbiome false-positive-control differential-expression 16s otu marker-gene-analysis relative-abundances compare-methods differential-abundance-methods

OmicsIntegrator2

Prize-Collecting Steiner Forests for Interactomes

✭ 40

Jupyter Notebook python proteomics omics steiner-tree prize-collecting

FALDO

Feature Annotation Location Description Ontology

✭ 28

XSLT genomics biology ontology proteomics uniprot

RforProteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

✭ 52

r tutorial bioconductor proteomics mass-spectrometry bioconductor-packages proteomics-data

compomics-utilities

Open source Java library for computational proteomics

✭ 24

java HTML bioinformatics proteomics computational-proteomics

QFeatures

Quantitative features for mass spectrometry data

✭ 12

r rstats bioconductor proteomics metabolomics mass-spectrometry

PAW pipeline

A Comet-based, best practices proteomics pipeline.

✭ 22

python comet proteomics protein-inference protein-identification tmt

pyqms

pyQms, generalized, fast and accurate mass spectrometry data quantification

✭ 22

python shell computational-biology proteomics metabolomics mass-spectrometry ms-data lipidomics

pFind3

No description or website provided.

✭ 20

bioinformatics proteomics mass-spectrometry peptide-identification

lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

LFQ-Analyst

The repo for LFQ-Analyst

✭ 17

HTML r statistical-analysis proteomics mass-spectrometry shinydashboard

pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

✭ 23

python cython semi-supervised-learning proteomics mass-spectrometry swath-ms openswath data-independent-acquisition

peptide-shaker

Interpretation of proteomics identification results

✭ 32

java HTML bioinformatics proteomics protein-identification

pia

📚 🔬 PIA - Protein Inference Algorithms

✭ 19

java search-engine inference protein proteomics protein-inference spectrum-identification

pDeep

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

✭ 24

python deep-learning proteomics mass-spectrometry

mokapot

Fast and flexible semi-supervised learning for peptide detection in Python

✭ 25

python Dockerfile machine-learning bioinformatics conda proteomics percolator peptide-detection

proteomics-metadata-standard

The Proteomics Experimental Design file format: Standard for experimental design annotation

✭ 49

python perl metadata proteomics proteomics-datasets multiomics proteomexchange sdrf pride-metadata msrun-metadata sdrf-proteomics proteomics-community proteomics-experiments mage-tab

PTXQC

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant

✭ 34

HTML r Batchfile quality-control drag-and-drop heatmap report proteomics metric openms hacktoberfest maxquant quality-metrics match-between-runs mztab

philosopher

A complete toolkit for shotgun proteomics data analysis

✭ 82

go bioinformatics data-analysis proteomics mass-spectrometry ms-data

cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

✭ 30

r CSS data-integration proteomics phosphoproteomics transcriptomics network-modelling metabolomic-data

OmicLearn

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

✭ 46

python Jupyter Notebook machine-learning bioinformatics proteomics omics biomarker-discovery

1-24 of 24 proteomics projects