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leonchaox/qinyan-academic-skills

188 skills · 11.5K combined installs

Skills from this source

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Skill
Source
8W Activity
Installs
1
cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or…
leonchaox/qinyan-academic-skills
61
2
clinicaltrials-database Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial det…
leonchaox/qinyan-academic-skills
61
3
clinpgx-database Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele f…
leonchaox/qinyan-academic-skills
61
4
clinvar-database Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classification…
leonchaox/qinyan-academic-skills
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5
cobrapy Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biolog…
leonchaox/qinyan-academic-skills
61
6
cosmic-database Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusi…
leonchaox/qinyan-academic-skills
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7
dask Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy co…
leonchaox/qinyan-academic-skills
61
8
datacommons-client Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use …
leonchaox/qinyan-academic-skills
61
9
datamol Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery …
leonchaox/qinyan-academic-skills
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10
deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), …
leonchaox/qinyan-academic-skills
61
11
diffdock Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual s…
leonchaox/qinyan-academic-skills
61
12
dnanexus-integration DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, …
leonchaox/qinyan-academic-skills
61
13
drugbank-database Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions,…
leonchaox/qinyan-academic-skills
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14
ena-database Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by a…
leonchaox/qinyan-academic-skills
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15
ensembl-database Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparat…
leonchaox/qinyan-academic-skills
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16
esm Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequenc…
leonchaox/qinyan-academic-skills
61
17
etetoolkit Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NC…
leonchaox/qinyan-academic-skills
61
18
fluidsim Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations incl…
leonchaox/qinyan-academic-skills
61
19
gene-database Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenot…
leonchaox/qinyan-academic-skills
61
20
geniml This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for tra…
leonchaox/qinyan-academic-skills
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21
geopandas Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when …
leonchaox/qinyan-academic-skills
61
22
get-available-resources This skill should be used at the start of any computationally intensive scientific task to detect and report availabl…
leonchaox/qinyan-academic-skills
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23
ginkgo-cloud-lab Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab…
leonchaox/qinyan-academic-skills
61
24
glycoengineering Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosyla…
leonchaox/qinyan-academic-skills
61
25
gnomad-database Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF),…
leonchaox/qinyan-academic-skills
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26
gtars High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic re…
leonchaox/qinyan-academic-skills
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27
gwas-database Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-va…
leonchaox/qinyan-academic-skills
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28
hmdb-database Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biom…
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29
hypogenic Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explo…
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interpro-database Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, …
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31
iso-13485-certification Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Syste…
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32
jaspar-database Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class;…
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33
kegg-database Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug …
leonchaox/qinyan-academic-skills
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34
labarchive-integration Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate wi…
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35
lamindb This skill should be used when working with LaminDB, an open-source data framework for biology that makes data querya…
leonchaox/qinyan-academic-skills
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36
latchbio-integration Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serve…
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37
matchms Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarit…
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38
medchem Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexit…
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39
metabolomics-workbench-database Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data,…
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40
modal Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running…
leonchaox/qinyan-academic-skills
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41
molecular-dynamics Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, def…
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42
monarch-database Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM,…
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43
opentargets-database Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetic…
leonchaox/qinyan-academic-skills
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44
pathml Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence…
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45
pdb-database Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/…
leonchaox/qinyan-academic-skills
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46
pennylane Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradien…
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47
phylogenetics Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (…
leonchaox/qinyan-academic-skills
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48
polars Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in mem…
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49
protocolsio-integration Integration with protocols.io API for managing scientific protocols. This skill should be used when working with prot…
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50
pubchem-database Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarit…
leonchaox/qinyan-academic-skills
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