Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: proteomics

Repositories

theGreatHerrLebert/rustims

A Framework for IMS-MS Raw Data Processing written in Rust and Python.

Language: Rust - Size: 36.9 MB - Last synced: 14 minutes ago - Pushed: about 23 hours ago - Stars: 4 - Forks: 1

Ainard09/protein_structure_predictor_app

Protein Predictor App

Language: Python - Size: 12.8 MB - Last synced: about 1 hour ago - Pushed: about 2 hours ago - Stars: 1 - Forks: 0

compomics/searchgui

Highly adaptable common interface for proteomics search and de novo engines

Language: Java - Size: 1.08 GB - Last synced: about 1 hour ago - Pushed: about 3 hours ago - Stars: 38 - Forks: 16

524D/mzrecal

Recalibrate Mass Spectrometry data in mzML format

Language: Go - Size: 6.22 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 6 - Forks: 0

moritzmadern/InterferenceModeling_in_MultiplexProteomics

Workflow to perform interference modeling and interference correction for MS2-based multiplex proteomics data

Language: R - Size: 42.5 MB - Last synced: about 7 hours ago - Pushed: about 8 hours ago - Stars: 1 - Forks: 1

wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

Language: Python - Size: 1.51 MB - Last synced: about 10 hours ago - Pushed: about 10 hours ago - Stars: 51 - Forks: 16

jinghuazhao/Caprion

Caprion pilot study

Language: HTML - Size: 2.97 MB - Last synced: about 17 hours ago - Pushed: about 19 hours ago - Stars: 1 - Forks: 0

A highly specialized suite of standardized plotting routines based on the "Grammar of Graphics" framework of mapping variables to aesthetics used in 'ggplot2'. Graphics types are biased towards visualizing SomaScan (proteomic) data.

Language: R - Size: 58.5 MB - Last synced: about 18 hours ago - Pushed: about 19 hours ago - Stars: 1 - Forks: 3

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 114 MB - Last synced: about 21 hours ago - Pushed: about 23 hours ago - Stars: 27 - Forks: 8

bigbio/quantms Fork of nf-core/quantms

Quantitative mass spectrometry workflow.

Language: Nextflow - Size: 46.9 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 17 - Forks: 6

uclahs-cds/package-moPepGen

Multi-Omics Peptide Generator

Language: Python - Size: 9.22 MB - Last synced: about 16 hours ago - Pushed: 1 day ago - Stars: 5 - Forks: 1

Vitek-Lab/MSstatsConvert

Converter functions for the MSstats package

Language: R - Size: 2.25 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 7 - Forks: 3

compomics/psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

Language: Python - Size: 104 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 20 - Forks: 6

Riley-Grindle/orthology_map

orthology_map is a pipeline designed to integrate suite of orthology assignment tools to contribute in a consensus based scoring algorithm

Language: Roff - Size: 25.4 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

hgb-bin-proteomics/MSAnnika_exporters

Export MS Annika crosslink results to different formats.

Language: Python - Size: 95.1 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

nf-core/quantms 📦

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

Language: Nextflow - Size: 21.5 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 26 - Forks: 28

hds-sandbox/proteomics-sandbox

A resource for biomedical students and researchers. Includes proteomics software tools like FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and PeptideShaker. Offers a user-friendly interface, automated identification and quantification, comprehensive data analysis, and lightweight clone feature for optimized storage.

Language: Dockerfile - Size: 5.14 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 6 - Forks: 1

YSHebron/scl-bioinfo

A bioinformatics project that aims to extend existing computational methods to predict (problematic) Protein Complexes from noisy PPINs and improve their performance.

Language: Perl - Size: 238 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

abelew/hpgltools Fork of elsayed-lab/hpgltools

A collection of R functions to aid in host-pathogen genomic research

Language: R - Size: 556 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 0

bioinfodlsu/phage-host-prediction

Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted sequence properties and eliminates the need to manually extract and select features from phage sequences

Language: Jupyter Notebook - Size: 10.9 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 9 - Forks: 2

MannLabs/OmicLearn Fork of OmicEra/OmicLearn

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

Language: Python - Size: 22.2 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 28 - Forks: 6

Nesvilab/philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

Language: Go - Size: 651 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 108 - Forks: 17

wilhelm-lab/dlomix

Python framework for Deep Learning in Proteomics

Language: Python - Size: 271 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 19 - Forks: 9

lightdock/lightdock

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

Language: Python - Size: 93 MB - Last synced: 3 days ago - Pushed: 4 months ago - Stars: 276 - Forks: 35

ScienceComputing/NGSOmics_Programming

Computational biology/bioinformatics workflows, codes, and concept notes on NGS data

Language: HTML - Size: 8.06 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 5 - Forks: 0

Metaboverse/Metaboverse

Visualization and analysis platform for metabolic data and network pattern recognition

Language: JavaScript - Size: 511 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 38 - Forks: 6

qzhang503/mzion

Proteomics database searches

Language: R - Size: 5.84 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

lazear/sage

Proteomics search & quantification so fast that it feels like magic

Language: Rust - Size: 9.11 MB - Last synced: 2 days ago - Pushed: 4 days ago - Stars: 194 - Forks: 38

MannLabs/alphapeptdeep

Deep learning framework for proteomics

Language: Jupyter Notebook - Size: 29.6 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 93 - Forks: 17

baynec2/mspms

R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data

Language: R - Size: 37.5 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

bigbio/pgt-pangenome

Protegenomics analysis based on Pangenome references

Language: Jupyter Notebook - Size: 569 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

lisiarend/PRONE

R Package for preprocessing, normalizing, and analyzing proteomics data

Language: R - Size: 40.4 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

lgatto/lgatto.github.io

My github page

Language: SCSS - Size: 115 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 9 - Forks: 11

sgibb/topdownrdata

Example data for the `topdown` R package

Language: R - Size: 117 MB - Last synced: 6 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

sgibb/talk-odense-20171127

Example files for talk in Odense 2017

Language: HTML - Size: 14.7 MB - Last synced: 6 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

wheretrue/exon

Exon is an OLAP query engine specifically for biology and life science applications.

Language: Rust - Size: 55.8 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 27 - Forks: 1

YogiOnBioinformatics/B-Cells-In-Atherosclerosis

Work done during rotation with Coleen McNamara & Stefan Bekiranov in UVA BIMS PhD program

Language: Jupyter Notebook - Size: 1.5 MB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

YogiOnBioinformatics/ChemInformatics-Machine-Learning-with-NNScore-2.0

Project in the Durrant Lab at UPitt that wanted to re-use code from a previous neural network ligand-protein interaction software to extract features for ML

Language: Python - Size: 48.8 KB - Last synced: 6 days ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

a-r-j/TB-Resources

List of online databases and resources for Mycobacterium Tuberculosis

Size: 10.7 KB - Last synced: 7 days ago - Pushed: about 5 years ago - Stars: 1 - Forks: 1

Karnovsky-Lab/DNEA

DNEA is an R package to construct data-driven biological networks from -omics data.

Language: R - Size: 45.1 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

JEFworks-Lab/CRAWDAD

Cell-type Relationship Analysis Workflow Done Across Distances

Language: R - Size: 946 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 11 - Forks: 1

lgatto/MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

Language: R - Size: 96.6 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 119 - Forks: 50

rformassspectrometry/Spectra

Low level infrastructure to handle MS spectra

Language: R - Size: 16.6 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 31 - Forks: 23

MannLabs/alphabase

Infrastructure of AlphaX ecosystem

Language: Jupyter Notebook - Size: 39.4 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 23 - Forks: 7

SysBioChalmers/GECKO

Toolbox for including enzyme constraints on a genome-scale model.

Language: MATLAB - Size: 105 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 61 - Forks: 42

UCLouvain-CBIO/LSTAT2340

Traitement statistique de données omiques

Language: HTML - Size: 21.9 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

Gagniuc/Visual-Sequence-Alignment-in-VB6

This highly visual and responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time.

Language: Visual Basic 6.0 - Size: 7.26 MB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 8 - Forks: 2

Francis-B/Kiwi

Fast regex-based protein digestion and unique peptides finder tool

Language: Python - Size: 6.83 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0

Vitek-Lab/MSstatsTMT

R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Language: R - Size: 61.2 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 26 - Forks: 13

Vitek-Lab/MSstatsPTM

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Language: R - Size: 21.4 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 7 - Forks: 2

SomaLogic/SomaScan.db

An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc.

Language: R - Size: 5.8 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 2 - Forks: 2

saramasarone/enrich_omics

A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

Language: Python - Size: 3.18 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 17 - Forks: 0

PyProphet/pyprophet

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

Language: Python - Size: 45.4 MB - Last synced: 12 days ago - Pushed: 4 months ago - Stars: 27 - Forks: 21

2n3m/2n3m

Biomedicine, Pharma, Life Science, IT Consulting

Size: 68.4 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

nara3m/nara3m

Nara Marella

Size: 30.3 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

compomics/ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

Language: Python - Size: 303 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 38 - Forks: 15

bigbio/py-pgatk

Python tools for proteogenomics analysis toolkit

Language: Python - Size: 125 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 9 - Forks: 11

glasgowcompbio/pyMultiOmics

Python toolbox for multi-omics data mapping and analysis

Language: Jupyter Notebook - Size: 45.9 MB - Last synced: 13 days ago - Pushed: about 1 year ago - Stars: 15 - Forks: 4

medbioinf/pia

:books: :microscope: PIA - Protein Inference Algorithms

Language: Java - Size: 49.5 MB - Last synced: 14 days ago - Pushed: 5 months ago - Stars: 20 - Forks: 9

ginkgobioworks/geckopy

Enzyme-constrained genome-scale models in python

Language: Python - Size: 4.84 MB - Last synced: 6 days ago - Pushed: 7 months ago - Stars: 23 - Forks: 4

CSi-Studio/ProPro-Server

DIA data analysis for Proteomics

Language: Java - Size: 20.2 MB - Last synced: 15 days ago - Pushed: over 2 years ago - Stars: 6 - Forks: 0

barsnes-group/peptide-shaker-online

Web-based framework for interactive visual analysis of proteomics data

Language: JavaScript - Size: 38.1 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 7 - Forks: 1

tnaake/MatrixQCvis

Language: R - Size: 4.47 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 5 - Forks: 1

shubhamkrpandey19/protein_toxicity_prediction

The prediction_script will enable you to predict whether your query protein sequence is cardiotoxic, neurotoxic, and/or enterotoxic.

Language: R - Size: 1.47 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 1

refresh-bio/FAMSA

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

Language: C - Size: 12.7 MB - Last synced: 4 days ago - Pushed: 9 days ago - Stars: 130 - Forks: 26

babessell1/MADRID Fork of HelikarLab/COMO

Metabolic Drug Repurposing Pipeline

Language: Python - Size: 733 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 4 - Forks: 0

BreisOne/rna-seq-proteomics-pipeline

Multi-omics analysis of LFQ proteomics and transcriptomics of an ALMS1 gene knockout cell model after TGF-B pathway stimulation.

Language: R - Size: 12 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

bigbio/proteomics-sample-metadata

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

Language: Python - Size: 96.4 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 72 - Forks: 106

rformassspectrometry/MsCoreUtils

Core Utils for Mass Spectrometry Data

Language: R - Size: 12.5 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 16 - Forks: 11

twoXes/awesome-structural-bioinformatics

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

Language: Python - Size: 31.1 MB - Last synced: 5 days ago - Pushed: about 1 year ago - Stars: 56 - Forks: 9

pgarrett-scripps/peptacular

A spectacularly simple package for working with peptide sequences.

Language: Python - Size: 11.3 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 8 - Forks: 0

compomics/reporter

Protein quantification based on reporter ions

Language: Java - Size: 32.1 MB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 4 - Forks: 2

compomics/peptide-shaker

Interpretation of proteomics identification results

Language: Java - Size: 182 MB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 45 - Forks: 20

bigbio/sdrf-pipelines

A repository to convert SDRF proteomics files into pipelines config files

Language: Python - Size: 2.47 MB - Last synced: 1 day ago - Pushed: about 1 month ago - Stars: 14 - Forks: 20

MannLabs/alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.

Language: HTML - Size: 204 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 154 - Forks: 28

jankod/DigestedProteinDB

Protein database digested with trypsin optimized for search by mass.

Language: Java - Size: 5.63 MB - Last synced: 21 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

soedinglab/plass

sensitive and precise assembly of short sequencing reads

Language: C - Size: 27 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 125 - Forks: 14

compomics/moFF

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

Language: Python - Size: 5.73 MB - Last synced: 22 days ago - Pushed: about 3 years ago - Stars: 32 - Forks: 11

anuragraj/PgxSAVy

A tool for quality control and annotation of variant peptides after FDR in proteogenomics

Language: Perl - Size: 1.98 MB - Last synced: 22 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

saezlab/cosmosR

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

Language: R - Size: 45.1 MB - Last synced: 23 days ago - Pushed: 5 months ago - Stars: 52 - Forks: 15

EMSL-Computing/IonToolPack

A software tool for omics-agnostic automated quality control of mass spectrometry data.

Language: Python - Size: 460 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 0 - Forks: 0

Nesvilab/FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

Language: Java - Size: 2.57 GB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 160 - Forks: 35

SomaLogic/SomaDataIO

The SomaDataIO package loads and exports 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' proprietary data file, called an ADAT ('*.adat'). The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.

Language: R - Size: 25.5 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 22 - Forks: 17