lobster-transcriptomics
Single-cell and bulk RNA-seq analysis agents for the Lobster AI platform.
Installation
pip install lobster-transcriptomics
Agents
| Agent | Description |
|---|---|
transcriptomics_expert |
Parent orchestrator for single-cell and bulk RNA-seq workflows. Handles QC, clustering, and coordinates sub-agents. |
annotation_expert |
Cell type annotation specialist. Automated and manual annotation, debris detection, annotation templates. |
de_analysis_expert |
Differential expression specialist. Pseudobulk aggregation, pyDESeq2, pathway enrichment. |
Services
| Service | Purpose |
|---|---|
| EnhancedSingleCellService | Single-cell clustering and analysis workflows |
| PseudobulkService | Aggregate single-cell data to pseudobulk for DE analysis |
| DifferentialFormulaService | Formula-based differential expression with pyDESeq2 |
| QualityService | Comprehensive QC metrics calculation and filtering |
| PreprocessingService | Normalization, log transformation, and preprocessing |
| ManualAnnotationService | Manual cluster annotation with template support |
| AnnotationTemplates | Tissue-specific marker gene templates (PBMC, brain, lung) |
| BulkVisualizationService | Publication-quality plots for bulk RNA-seq results |
Features
- Auto-detection of single-cell vs bulk RNA-seq data types
- Comprehensive QC metrics including gene counts, mitochondrial %, and ribosomal %
- Flexible filtering with data-type-appropriate default thresholds
- Leiden clustering with multi-resolution support and quality metrics
- UMAP visualization with automatic point size scaling
- Deviance-based highly variable gene selection
- Batch correction for multi-sample experimental designs
- Sub-clustering for heterogeneous cell populations
- Tissue-specific annotation templates for rapid cell type identification
- Pseudobulk aggregation from single-cell to bulk format
- Formula-based DE analysis supporting complex experimental designs
- GO and KEGG pathway enrichment for biological interpretation
Requirements
- Python 3.12+
- lobster-ai >= 1.0.0
Documentation
Full documentation: docs.omics-os.com/docs/agents/transcriptomics
License
MIT
1 maintainer
Metadata
1 maintainer
Release files for lobster-transcriptomics 1.1.429
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| lobster_transcriptomics-1.1.429.tar.gz | 180.1 kB | With provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| lobster_transcriptomics-1.1.429-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 368.1 kB
Release files / lobster_transcriptomics-1.1.429.tar.gz
| Download URL | lobster_transcriptomics-1.1.429.tar.gz |
|---|---|
| Size | 180.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
7e56f725ec48a9bb358af114490849da1eb114a0a099077fefd61afc10c869f4
|
|
BLAKE2b-256 checksum How to use checksums |
dbb4e839fe0d3f9897a65bb6e1a8f135c10831c7c5c6bab615ff5e289f845cf9
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 21, 2026.
Transparency logRelease files / lobster_transcriptomics-1.1.429-py3-none-any.whl
| Download URL | lobster_transcriptomics-1.1.429-py3-none-any.whl |
|---|---|
| Size | 188.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
d1a866d4a4ba3626e07f2c65557a306481faa34228d8a7b7d4588b950dd5be81
|
|
BLAKE2b-256 checksum How to use checksums |
4738fc92210dc55171dc508638fedd8de759d692bf0585122d9048e9107c711a
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 21, 2026.
Transparency logSecurity for lobster-transcriptomics 1.1.429
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
Full provenance
All 2 files in this release have been uploaded with provenance metadata.
Attestation for lobster_transcriptomics-1.1.429.tar.gz
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 21, 2026.
Transparency logA note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
