https://github.com/k-dense-ai/scientific-agent-skills

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 138 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Antigravity, and the open Agent Skills standard.

agent-skills ai-scientist bioinformatics chemoinformatics claude claude-skills claudecode clinical-research computational-biology data-analysis drug-discovery genomics materials-science metabolomics proteomics scientific-computing scientific-visualization

Last synced: 28 May 2026

https://github.com/scverse/gget

🧬 gget enables efficient querying of genomic reference databases

alphafold alphafold2 archs4 blast cellxgene databases enrichment-analysis enrichr ensembl genomics gget ncbi proteomics reference rna-seq transcriptomics uniprot

Last synced: 28 Jun 2026

https://github.com/pachterlab/gget

🧬 gget enables efficient querying of genomic reference databases

alphafold alphafold2 archs4 blast databases enrichment-analysis enrichr ensembl genomics gget ncbi proteomics reference rna-seq transcriptomics uniprot

Last synced: 27 Feb 2026

https://github.com/OpenMS/OpenMS

The codebase of the OpenMS project

3-clause-bsd algorithms analyses c-plus-plus hacktoberfest linux macos mass-spectrometry metabolomics ms-data openms proteomics windows

Last synced: 12 Sep 2025

https://github.com/openms/openms

The codebase of the OpenMS project

3-clause-bsd algorithms analyses c-plus-plus hacktoberfest linux macos mass-spectrometry metabolomics ms-data openms proteomics windows

Last synced: 14 May 2025

https://github.com/galaxyproject/training-material

A collection of Galaxy-related training material

chip-seq hacktoberfest materials metagenomics ngs proteomics rnaseq training tutorial usegalaxy

Last synced: 15 May 2025

https://github.com/tariqdaouda/pygeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

Last synced: 09 Oct 2025

https://github.com/tariqdaouda/pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

Last synced: 30 Mar 2025

https://github.com/lazear/sage

Proteomics search & quantification so fast that it feels like magic

bioinformatics mass-spectrometry proteomics

Last synced: 28 Jan 2026

https://github.com/Nesvilab/FragPipe

A cross-platform proteomics data analysis suite

command-line-interface data-dependent-acquisition data-independent-acquisition gui isobaric-quantification label-free-quantification mass-spectrometry proteomics

Last synced: 30 Apr 2025

https://github.com/lgatto/teachingmaterial

Various teaching material

data-analysis make makefile oo-programming programming-tutorial proteomics r statistics teaching-materials vectorisation visualisation

Last synced: 08 May 2025

https://github.com/mannlabs/alphapept

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

alphapept-ecosystem bioinformatics mass-spectrometry proteomics

Last synced: 14 Dec 2025

https://github.com/soedinglab/plass

sensitive and precise assembly of short sequencing reads

bioinformatics metagenomics metatranscriptomics opensource proteins proteomics sequence-assembler

Last synced: 04 Apr 2025

https://github.com/lgatto/msnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 15 May 2025

https://github.com/lgatto/MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 30 Apr 2025

https://github.com/Nesvilab/philosopher

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

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

Last synced: 19 Apr 2025

https://github.com/bigbio/proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

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

Last synced: 17 Jan 2026

https://github.com/mrzresearcharena/pyfeat

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

bioinformatics computational-biology genomics proteomics

Last synced: 14 Apr 2025

https://github.com/lgatto/rforproteomics

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

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

Last synced: 17 Mar 2025

https://github.com/wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

deep-learning framework mass-spectrometry metabolomics proteomics pytorch

Last synced: 31 May 2026

https://github.com/BioTender-max/awesome-bio-agent-skills

A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.

agent-skills ai-agent ai-agents awesome awesome-list bioinformatics biomedical claude claude-code claude-skills computational-biology drug-discovery genomics llm mcp protein-design proteomics single-cell skills transcriptomics

Last synced: 24 Jun 2026

https://github.com/sysbiochalmers/gecko

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

data-integration enzyme-constraints kinetics matlab proteomics systems-biology toolbox

Last synced: 24 Oct 2025

https://github.com/jpquast/protti

Picotti lab data analysis package.

data-analysis lip-ms mass-spectrometry omics protein proteomics r systems-biology

Last synced: 16 Jan 2026

https://github.com/compomics/DeepLC

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

deep-learning peptide-modification peptides proteomics retention-time

Last synced: 30 Apr 2025

https://github.com/saezlab/cosmosr

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

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

Last synced: 09 Apr 2025

https://github.com/wilhelm-lab/koina

Democratizing ML in proteomics

bioinformatics deep-learning machine-learning mass-spectrometry proteomics python

Last synced: 19 Feb 2026

https://github.com/microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

ecoinformatics fair-data genomics linkml metabolomics metadata microbiome microbiomedata mixs nmdc proteomics samples schema standards transcriptomics

Last synced: 10 Jun 2026

https://github.com/wfondrie/mokapot

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

bioinformatics conda machine-learning peptide-detection percolator proteomics python

Last synced: 05 Apr 2025

https://github.com/mikelkou/fava

Functional Associations using Variational Autoencoders

co-expression deep-learning networks networks-biology proteomics single-cells

Last synced: 12 Mar 2026

https://github.com/endixk/ezaai

EzAAI - High Throughput Prokaryotic AAI Calculator

comparative-genomics genomics prokaryotic-genomes proteomics

Last synced: 11 Jul 2025

https://github.com/ursgal/ursgal

Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis

mass-spectrometry ms-data mzml omics peptide-identification proteomics proteomics-data python

Last synced: 30 Apr 2025

https://github.com/wilhelm-lab/dlomix

Python framework for Deep Learning in Proteomics

deep-learning framework machine-learning mass-spectrometry peptide-sequences peptides proteomics

Last synced: 12 Feb 2026

https://github.com/rformassspectrometry/spectra

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 04 Apr 2025

https://rformassspectrometry.github.io/Spectra/

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 13 Apr 2025

https://github.com/pwilmart/paw_pipeline

A Comet-based, best practices proteomics pipeline.

comet protein-identification protein-inference proteomics python3 tmt

Last synced: 25 Jul 2025

https://github.com/pwilmart/PAW_pipeline

A Comet-based, best practices proteomics pipeline.

comet protein-identification protein-inference proteomics python3 tmt

Last synced: 30 Apr 2025

https://github.com/compomics/meta-proteome-analyzer

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

bioinformatics-pipeline database-searchtool metaproteomics protein-identification proteomics software

Last synced: 10 Feb 2026

https://github.com/bigbio/pmultiqc

A library for QC report based on MultiQC framework

mass-spectrometry proteomics proteomics-data qc qc-proteomics

Last synced: 02 Apr 2026

https://github.com/Vitek-Lab/MSstatsTMT

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

labeling mass-spectrometry msstats proteomics tmt tmt-data-analysis

Last synced: 30 Apr 2025

https://github.com/rformassspectrometry/qfeatures

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 06 Apr 2025

https://github.com/ginkgobioworks/geckopy

Enzyme-constrained genome-scale models in python

data-integration enzyme-constraints kinetics omics proteomics systems-biology thermodynamics

Last synced: 25 Oct 2025

https://github.com/the-omics-os/lobster

The self-evolving agentic framework for bioinformatics

agents bioinformatics langgraph lobster omics proteomics transcriptomics

Last synced: 25 Apr 2026

https://github.com/kusterlab/curve_curator

Analysis platform for large-scale dose-dependent data

analysis bioinformatics curve-fitting dashboard decrypte decryptm dose-response p-value proteomics statistics viability

Last synced: 17 Mar 2026

https://rformassspectrometry.github.io/QFeatures/

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 13 Apr 2025

https://github.com/opencog/agi-bio

Genomic and Proteomic data exploration and pattern mining

artificial-intelligence genetic-analysis genetics genomics protein-sequences proteomics

Last synced: 01 Mar 2026

https://github.com/snijderlab/annotator

A simple tool to help you manually discover the depths of your (complex) spectra, one spectrum at a time.

cross-linking glycans mass-spectrometry proteomics

Last synced: 13 Jun 2025

https://github.com/rusteomics/mzcore

A Rust library for parsing ProForma peptides and matching them against MS spectra, formally known as rustyms

chemistry mass-spectrometry proforma proteomics rust

Last synced: 12 Dec 2025

https://github.com/compomics/thermorawfileparsergui

Graphical user interface for the ThermoRawFileParser

conversion java proteomics raw

Last synced: 10 Feb 2026

https://github.com/pwilmart/tmt_analysis_examples

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.

ipynb jupyter-notebook mass-spectrometry proteomics proteomics-data r tmt tmt-data-analyses

Last synced: 28 Oct 2025

https://github.com/pixelgentechnologies/pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

molecular-pixelation pixelgen-technologies protein proteomics proximity-network single-cell single-cell-omics spatial

Last synced: 29 May 2026

https://github.com/mmasoud1/histojs

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

cell-cell-interaction cell-segmentation digital-slide-archive image-processing mibiscope multichannel multiplexed-imaging multiplexed-imaging-analysis ome-tiff phenotyping proteomics proteomics-data-analysis single-cell spatial-biology spatial-data-analysis whole-slide-imaging

Last synced: 15 Oct 2025

https://github.com/jdrudolph/photon

PHOsphoproteomic dissecTiOn using Networks

bioinformatics biological-data-analysis biology pathways phosphoproteomics phosphorylation proteomics signaling-networks signaling-pathways

Last synced: 11 Feb 2026

https://github.com/pcastellanoescuder/pomashiny

:apple: Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis

bioinformatics exploratory-data-analysis gui mass-spectrometry metabolomics pre-processing proteomics r shiny shiny-apps shinydashboard statistical-analysis visualization

Last synced: 28 Oct 2025

https://github.com/lgatto/proloc

A unifying bioinformatics framework for organelle proteomics

bioconductor proteomics proteomics-data r spatial-proteomics visualisation

Last synced: 06 Apr 2025

https://github.com/rformassspectrometry/mscoreutils

Core Utils for Mass Spectrometry Data

bioconductor mass-spectrometry metabolomics proteomics rstats utils

Last synced: 06 Apr 2025

https://github.com/caranathunge/promor

A comprehensive R package for label-free proteomics data analysis and modeling

biomarkers differential-expression lfq machine-learning mass-spectrometry modeling proteomics r r-package rstats

Last synced: 24 Sep 2025

https://rformassspectrometry.github.io/MsCoreUtils/

Core Utils for Mass Spectrometry Data

bioconductor mass-spectrometry metabolomics proteomics rstats utils

Last synced: 13 Apr 2025

https://github.com/bigbio/ibaqpy

Absolute quantification package based on quantms.io

absolute-quantification ibaq mass-spectrometry proteomics quantification

Last synced: 14 Jan 2026

https://github.com/thegreatherrlebert/ionmob

An open-source prediction framework for peptide ion collision cross section (CCS) values with python.

ccs collisional-cross-section deep-learning ion-mobility ion-mobility-spectrometry machine-learning mass-spectrometry proteomics pypi python-package

Last synced: 08 Oct 2025

https://github.com/sbl-sdsc/mmtf-proteomics

Methods for mapping proteomics data on 3D protein structure.

binder jupyter-notebook protein-data-bank proteomics pyspark

Last synced: 12 Apr 2025

https://github.com/cran-task-views/omics

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

cran genomics metabolomics omics proteomics r rstats task-views transcriptomics

Last synced: 13 Apr 2025

https://github.com/pwilmart/irs_normalization

An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.

ipynb irs-normalization jupyter-notebook mass-spectrometry normalization proteomics proteomics-data r tmt

Last synced: 28 Oct 2025

https://github.com/bigbio/nf-workflows

Repository of Nextflow+BioContainers workflows

biocontainers bioinformatics bioinformatics-pipeline nextflow proteomics workflow

Last synced: 17 Jan 2026

https://github.com/bamescience/mistle

Mistle is a fast spectral search engine. It uses a fragment-indexing technique and SIMD intrinsics to match experimental MS2 spectra to large spectral libraries at a high performance.

algorithm metaproteomics proteomics spectral-library tandem-ms

Last synced: 23 Aug 2025

https://github.com/bigbio/py-pgatk

Python tools for proteogenomics analysis toolkit

ensembl mass-spectrometry proteogenomics proteogenomics-analysis-toolkit proteomics python vcf

Last synced: 17 Jan 2026

https://github.com/becavin-lab/bacnet

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

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

Last synced: 09 Apr 2026

https://github.com/delosh653/echo

An application to find and visualize circadian rhythms in time course data using extended harmonic oscillators.

bioinformatics bioinformatics-tool circadian circadian-rhythm circadian-rhythmicity echo extended-harmonic-oscillators finding-rhythms omics oscillators proteomics transcriptomics

Last synced: 11 Apr 2025

https://github.com/rformassspectrometry/book

R for Mass Spectrometry documentation

documentation mass-spectrometry metabolomics proteomics

Last synced: 07 Mar 2026

https://github.com/maayanlab/playbook-workflow-builder

A repository for the Playbook Workflow Builder project.

bioinformatics biology cwl data-science gene-expression gene-ontology gene-sets proteomics rna-seq-analysis systems-biology workflow

Last synced: 11 Jul 2025

https://github.com/cpanse/protviz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

cran fun mass-spectrometry peptide-identification proteomics quantification rstats visualization

Last synced: 10 Apr 2026

https://github.com/pnnl-comp-mass-spec/proteomics-data-analysis-tutorial

A comprehensive tutorial for proteomics data analysis in R that utilizes packages developed by researchers at PNNL and from Bioconductor.

data-analysis proteomics

Last synced: 18 Jan 2026

https://github.com/thegreatherrlebert/rustims

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

bottom-up data-independent-acquisition high-throughput ion-mobility-spectrometry mass-spectrometry omics proteomics pyo3 python raw-data rust-lang timstof

Last synced: 16 May 2025

https://github.com/lgatto/lgatto.github.io

My github page

bioinformatics blog computational-biology programming proteomics r research science

Last synced: 21 Mar 2025

https://github.com/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.

dna dna-sequences gap genetics genomics global heatmap match matrix mismatch proteomics rna score sequence-alignment traceback visualization

Last synced: 06 Mar 2026

https://github.com/mrzresearcharena/pyfeat-2.x

Biological Feature Representation Tool form the Sequences

bioinformatics computational-biology genomics proteomics rna-seq

Last synced: 19 Jan 2026

https://github.com/czbiohub-sf/protdata

Dataloader for common proteomics search engine outputs into AnnData format

anndata proteomics proteomics-datasets python

Last synced: 16 Jan 2026

https://github.com/sysbiochalmers/orthomics

Collection of scripts for gene age sorting and multi-omics data mining and analysis

data-integration data-visualization de-analysis orthology proteomics rnaseq

Last synced: 07 Mar 2026

https://github.com/pgarrett-scripps/peptacular

A spectacularly simple package for working with peptide sequences.

bioinformatics mass-spectrometry peptide-identification peptide-sequences peptides protein proteomics python

Last synced: 31 Jul 2025

https://github.com/daisybio/prone

R Package for preprocessing, normalizing, and analyzing proteomics data

data-analysis evaluation normalization proteomics

Last synced: 25 May 2026

https://github.com/paccmann/paccmann_omics

Generative models for transcriptomics profiles and proteins

deep-learning generative-model proteomics transcriptomics vae variational-autoencoder

Last synced: 10 Apr 2025

https://github.com/bzhanglab/deeprescore

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

deep-learning machine-learning msms peptide-identification proteomics

Last synced: 07 Feb 2026

https://github.com/rformassspectrometry/unimod

Amino acid modifications for mass spectrometry

amino-acid-modifications mass-spectrometry protein proteomics r

Last synced: 27 Oct 2025

https://github.com/dev-ev/ms-interactive-viz

Customizable and informative mass spectra with Bokeh

bokeh interactive-visualizations mass-spectrometry proteomics visualization

Last synced: 16 Jul 2025

https://github.com/pwilmart/paw_blast

A utility for blasting one protein FASTA file against another FASTA file to find orthologs.

annotations blast proteomics python3

Last synced: 28 Oct 2025

https://github.com/tnaake/msquality

mass-spectrometry metabolomics proteomics qc r

Last synced: 23 Jun 2025

https://github.com/rformassspectrometry/protgenerics

S4 generic functions for Bioconductor mass spectrometry infrastructure

bioconductor mass-spectrometry metabolomics proteomics r

Last synced: 08 Aug 2025

https://github.com/dmmiller612/correlation-gcn

Correlation Graph Convolutional Networks on Gene Expression and other Biology data

deep-learning gcn gene gene-expression graph graph-convolutional-network proteomics tensorflow

Last synced: 29 Oct 2025

https://github.com/talusbio/nf-encyclopedia

A NextFlow pipeline for chromatogram library DIA proteomics workflows

bioinformatics data-independent-acquisition nextflow pipeline proteomics workflow

Last synced: 18 Jan 2026

https://github.com/br3ndonland/r-proteomics-nrf1

Molecular biology experiments, mass spectrometry-based proteomics, and reproducible data analysis in R

binder jupyter jupyter-notebook mass-spectrometry protein-protein-interaction proteomics proteomics-data r reproducibility reproducibility-crisis reproducible-research rmarkdown rstudio science

Last synced: 05 Apr 2025

https://github.com/bigbio/quantms-utils

A python library with scripts and helpers classes for quantms workflow

bigdata cloud mass-spectrometry nextflow proteogenomics proteomics

Last synced: 08 Apr 2026

https://github.com/pwilmart/annotations

GUI tool to add rich annotations to PAW summary files from Swiss-Prot flat text files.

orthologs protein-annotations proteomics python3 tkinter-gui

Last synced: 05 Sep 2025

https://github.com/linas/biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes

genomic-data-analysis genomics-visualization proteogenomics proteomics reactome reactome-pathway

Last synced: 03 Jan 2026

https://github.com/mansanlab/alphafoldfetch

A tool for downloading AlphaFold structures using UniProt IDs or FASTA files

ai alphafold bioinformatics computational-biology ml proteomics

Last synced: 02 Apr 2026

https://github.com/pwilmart/irs_validation

Analysis of technical replicate channels to more fully validate the internal reference scaling (IRS) method.

ipynb irs irs-normalization jupyter-notebook normalization proteomics r tmt tmt-data-analyses

Last synced: 28 Oct 2025

https://github.com/jamiemcg/comparesequences

Generates plots to compare properties of protein sequences from different FASTA files

bioinformatics genomics proteomics visualization

Last synced: 13 Oct 2025

https://github.com/grosenberger/secat

Size-Exclusion Chromatography Algorithmic Toolkit

data-independent-acquisition machine-learning mass-spectrometry proteomics signal-processing size-exclusion-chromatography swath-ms

Last synced: 19 Apr 2025

https://github.com/dev-ev/isobaric-prot-wf-r

Simple workflows for the isobaric-labeling proteomic data from Proteome Discoverer with ANOVA, t-testing, DEqMS/limma and annotation via fgsea

data-visualization deqms limma proteomics proteomics-data statistical-analysis tmt-data-analysis

Last synced: 13 Aug 2025

https://github.com/gagniuc/sequence-logo-relative-style

Sequence Logo - relative style is an alternative that provides full control over how the graphics of a Sequence Logo should look like, and is an alternative to an application called WebLogo. All the inner workings of this open source application are written in native javascript.

dna dna-processing html-css-javascript html5 html5-canvas javascript js motif proteomics rna-sequences sequence-logo

Last synced: 14 Aug 2025

https://github.com/pgarrett-scripps/fastaframes

Python package to convert between FASTA files and Pandas DataFrames.

bioinformatics fasta mass-spectrometry package pandas protein protein-sequences proteomics python

Last synced: 31 Jul 2025

https://github.com/fcyu/pipi

PTM-Invariant Peptide Identification. An open search tool.

peptide-identification proteomics ptm-identification

Last synced: 19 Apr 2025