Proteomics agent for Lobster AI (DDA/DIA mass spectrometry, affinity platforms)

Navigation

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for cewinharhar from gravatar.com cewinharhar

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License Expression: AGPL-3.0-or-later
    SPDX License Expression
  • Author: Omics-OS
  • Tags bioinformatics , proteomics , mass-spectrometry , DDA , DIA , Olink , SomaScan , lobster-ai
  • Requires: Python <3.14, >=3.12
  • Provides-Extra: network-analysis
Classifiers
Report project as malware

Project description

lobster-proteomics

Unified proteomics analysis for mass spectrometry (DDA/DIA) and affinity platforms (Olink, SomaScan).

Installation

pip install lobster-proteomics

Agents

Agent Description
proteomics_expert Full proteomics workflow orchestration with auto-detection of platform type and appropriate preprocessing.

Services

Service Purpose
ProteomicsAnalysisService Core analysis workflows for protein quantification
ProteomicsDifferentialService Differential protein expression between conditions
ProteomicsSurvivalService Survival analysis with protein biomarkers
ProteomicsNetworkService Protein-protein interaction network analysis
ProteomicsQualityService Quality control and missing value assessment
ProteomicsPreprocessingService MNAR/MAR-aware imputation and normalization
ProteomicsVisualizationService Volcano plots, heatmaps, and network graphs
MaxQuantParser Parse MaxQuant proteinGroups.txt output
DIANNParser Parse DIA-NN report.tsv output
SpectronautParser Parse Spectronaut report output
OlinkParser Parse Olink NPX export files

Features

  • Auto-detection of platform type from data characteristics
  • Missing value handling optimized for MNAR (mass spec) vs MAR (affinity) patterns
  • Platform-appropriate quality control with batch effect detection
  • Median and quantile normalization with log2 transformation
  • Multiple imputation strategies (MinDet, KNN, zero, median)
  • Differential protein analysis with multiple testing correction
  • Volcano plots and MA plots for results visualization
  • Protein-protein interaction network construction and visualization
  • Survival analysis integration for clinical proteomics studies
  • Support for multi-plex affinity platforms (Olink, SomaScan, Luminex)

Platform Support

Platform Missing Values Normalization Notes
Mass Spectrometry (DDA/DIA) 30-70% (MNAR) Median + log2 Peptide mapping support
Affinity (Olink) <30% (MAR) Quantile Plate effect correction
Affinity (SomaScan) <30% (MAR) Quantile Antibody validation

Requirements

  • Python 3.12+
  • lobster-ai >= 1.0.0

Tier Requirement

This is a free agent. Access is controlled at runtime via Lobster AI's tier system.

Documentation

Full documentation: docs.omics-os.com/docs/agents/proteomics

License

MIT

Project details

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for cewinharhar from gravatar.com cewinharhar

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License Expression: AGPL-3.0-or-later
    SPDX License Expression
  • Author: Omics-OS
  • Tags bioinformatics , proteomics , mass-spectrometry , DDA , DIA , Olink , SomaScan , lobster-ai
  • Requires: Python <3.14, >=3.12
  • Provides-Extra: network-analysis
Classifiers

Release history Release notifications | RSS feed

1.1.418

1.1.411

1.1.408

This version

1.1.407

1.1.406

1.1.404

1.1.403

1.1.2

1.1.1

1.0.11

1.0.10

1.0.9

1.0.8

1.0.1

1.0.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

lobster_proteomics-1.1.407.tar.gz (186.3 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

lobster_proteomics-1.1.407-py3-none-any.whl (204.9 kB view details)

Uploaded Python 3

File details

Details for the file lobster_proteomics-1.1.407.tar.gz.

File metadata

  • Download URL: lobster_proteomics-1.1.407.tar.gz
  • Upload date:
  • Size: 186.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.7

File hashes

Hashes for lobster_proteomics-1.1.407.tar.gz
Algorithm Hash digest
SHA256 c98ddc78e104a58a8402facadab57fdd335c71b4842c6428025319edc846e5e1
MD5 2e273a3b267057d4a9f16edaedd080d4
BLAKE2b-256 83186e0ff4992b6847b87ff1ccae6c3361dad08eceac0aea0601b05bdab656ba

See more details on using hashes here.

Provenance

The following attestation bundles were made for lobster_proteomics-1.1.407.tar.gz:

Publisher: publish-packages.yml on the-omics-os/lobster

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file lobster_proteomics-1.1.407-py3-none-any.whl.

File metadata

File hashes

Hashes for lobster_proteomics-1.1.407-py3-none-any.whl
Algorithm Hash digest
SHA256 87eeafb7e3b6d703588fd2a0bd65ac8a8a0f99f0fcabd48bb495657e8ab26e8a
MD5 7f62b46a75f3982e23d2ee9d426edb4a
BLAKE2b-256 73602026ca5aca40358c788aa217924a027ed08ab248e01d563fee301b7c0c1c

See more details on using hashes here.

Provenance

The following attestation bundles were made for lobster_proteomics-1.1.407-py3-none-any.whl:

Publisher: publish-packages.yml on the-omics-os/lobster

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page