GitHub
text-analyst
Computational text analysis for sociology research using R or Python. Guides you through topic models, sentiment analysis, classification, and embeddings with systematic validation. Supports both traditional (L...
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分类目录: databases bioinformatics
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GitHub
gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment...
☆ 9查看技能
GitHub
networkx
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing gra...
☆ 9查看技能
GitHub
pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal pro...
☆ 9查看技能
GitHub
discopy
DisCoPy: Python library for computing with string diagrams - monoidal
☆ 5查看技能
GitHub
pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
☆ 3查看技能
GitHub
kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices...
☆ 3查看技能
GitHub
networkx
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing gra...
☆ 3查看技能
GitHub
gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment...
☆ 3查看技能
GitHub
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID map...
☆ 3查看技能
GitHub
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
☆ 3查看技能
GitHub
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch...
☆ 3查看技能
GitHub
omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
☆ 3查看技能
GitHub
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use thi...
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GitHub
biopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioin...
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GitHub
rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, pro...
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GitHub
airalogy-protocol
Expert guide for creating Airalogy Protocols (AIMD), Assigners (Python logic), and Validation Models. Use this to design digital workflows and experiments.
☆ 1查看技能
GitHub
life-sciences-connector
Query PubMed and scientific databases for protocols, analyze biological data with Biopython, handle HIPAA-compliant data. Use for biology research, protocol searches, sequence analysis, or scientific data handl...
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GitHub
bio-blast
NCBI BLAST sequence similarity search using BioPython. Use when a user wants to run BLAST programmatically with blastn/blastp and retrieve results in JSON format.
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GitHub
tree-visualization
Comprehensive guide to phylogenetic tree visualization including matplotlib (Python), ggtree (R), and publication-quality figure generation. Covers rectangular, circular, radial layouts, bootstrap annotations,...
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GitHub
scanpy-single-cell-analysis
Python-based single cell analysis using Scanpy for .h5ad files in conda scanpy environment
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GitHub
spatialdata
SpatialData framework for handling spatial multi-modal and multi-scale data. Use this skill for questions about spatial omics data analysis, visualization, and the SpatialData Python ecosystem.
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GitHub
envi-pkg-local-improved
ENVI spatial transcriptomics analysis toolkit - comprehensive documentation with tutorials and Python source code
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GitHub
neuroimaging-qc
Evidence-based QC decision-making for neuroimaging data. Interpret QC metrics from any pipeline (fMRIPrep, MRIQC, FreeSurfer, MNE-Python, Homer3, custom outputs) to make justified inclusion/exclusion decisions....
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