Skills

github.com/synthetic-sciences/openscience4.3k

openscience

The open-source AI workbench for scientific research

npx skills add synthetic-sciences/openscience -g -y
synthetic-sciences/openscience preview
40 skills

AnnData Single-Cell Data

Reads and writes annotated matrices and h5ad files in single-cell analysis.

synthetic-sciences/openscience4.3k

Benchling Integration

Benchling R&D platform integration.

synthetic-sciences/openscience4.3k

Bids

Use this skill when working with Brain Imaging Data Structure (BIDS) datasets...

synthetic-sciences/openscience4.3k

Bioimage Analysis

Microscopy image analysis for cell biology.

synthetic-sciences/openscience4.3k

Bionemo Nims

Run NVIDIA BioNeMo NIMs through the hosted scientific_capability tool with your own...

synthetic-sciences/openscience4.3k

Biopython

Comprehensive molecular biology toolkit.

synthetic-sciences/openscience4.3k

Bioservices

Unified Python interface to 40+ bioinformatics services.

synthetic-sciences/openscience4.3k

Bulk Rnaseq

End-to-end bulk RNA-seq orchestrator, takes raw FASTQ reads through QC and trimming...

synthetic-sciences/openscience4.3k

Bun File Io

Use this when you are working on file operations like reading, writing, scanning, or...

synthetic-sciences/openscience4.3k

Cancer Genomics Analysis

Computational cancer genomics workflows.

synthetic-sciences/openscience4.3k

Clinical Decision Support

Generate professional clinical decision support (CDS) documents for pharmaceutical and...

synthetic-sciences/openscience4.3k

Clinical Imaging

Clinical and physiological imaging analysis.

synthetic-sciences/openscience4.3k

Clinical Reports

Write comprehensive clinical reports including case reports (CARE guidelines)...

synthetic-sciences/openscience4.3k

Cobrapy

Constraint-based metabolic modeling (COBRA).

synthetic-sciences/openscience4.3k

Curated Bio Datasets

Guide to accessing curated biological datasets for computational biology.

synthetic-sciences/openscience4.3k

Deepspot M

Generate transcriptome-wide virtual spatial transcriptomics from H&E histology with...

synthetic-sciences/openscience4.3k

Dnanexus Integration

DNAnexus cloud genomics platform.

synthetic-sciences/openscience4.3k

Esm

Comprehensive toolkit for protein language models including ESM3 (generative multimodal...

synthetic-sciences/openscience4.3k

Etetoolkit

Phylogenetic tree toolkit (ETE).

synthetic-sciences/openscience4.3k

Flow Cytometry Analysis

Complete flow cytometry analysis pipeline.

synthetic-sciences/openscience4.3k

Flowio

Parse FCS (Flow Cytometry Standard) files v2.0-3.1.

synthetic-sciences/openscience4.3k

Folklore Variant Evidence

Retrieve ClinGen gene-disease validity assertions for a public gene or disease, and...

synthetic-sciences/openscience4.3k

Genomic Coordinates

Convert genomic intervals between coordinate conventions, normalise and compare variant...

synthetic-sciences/openscience4.3k

Genomic Intelligence

Predict regulatory features, gene structure, and expression directly from DNA sequence...

synthetic-sciences/openscience4.3k

Gget

Fast CLI/Python queries to 20+ bioinformatics databases.

synthetic-sciences/openscience4.3k

Ginkgo Cloud Lab

Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a...

synthetic-sciences/openscience4.3k

Glycobiology

Glycosylation site prediction and glycobiology analysis.

synthetic-sciences/openscience4.3k

Glycoengineering

Analyze and engineer protein glycosylation.

synthetic-sciences/openscience4.3k

Histolab

Lightweight WSI tile extraction and preprocessing.

synthetic-sciences/openscience4.3k

Immunology Assays

Computational analysis of immunology experimental data.

synthetic-sciences/openscience4.3k

Lamindb

Should be used when working with LaminDB, an open-source data framework for biology...

synthetic-sciences/openscience4.3k

Latchbio Integration

Latch platform for bioinformatics workflows.

synthetic-sciences/openscience4.3k

Marker Panel Annotation

Assigns cell-type labels to clusters from a protein marker panel (multiplexed imaging...

synthetic-sciences/openscience4.3k

Microbial Dynamics

Microbial population dynamics modeling and analysis.

synthetic-sciences/openscience4.3k

Molecular Cloning

Molecular cloning simulation and design.

synthetic-sciences/openscience4.3k

Neurokit2

Comprehensive biosignal processing toolkit for analyzing physiological data including...

synthetic-sciences/openscience4.3k

Neuropixels Analysis

Neuropixels neural recording analysis.

synthetic-sciences/openscience4.3k

Nextflow

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end.

synthetic-sciences/openscience4.3k

Omero Integration

Microscopy data management platform.

synthetic-sciences/openscience4.3k

Opentrons Integration

Official Opentrons Protocol API for OT-2 and Flex robots.

synthetic-sciences/openscience4.3k