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Latch Bioinformatics Workflows

latchbio-integration

K-Dense-AI/claude-scientific-skills

LatchBio Integration provides a Python-first platform to compose, deploy, and monitor serverless bioinformatics pipelines with the Latch SDK, decorator-based tasks, cloud storage (LatchFile/Dir), GPU tuning, and Nextflow or Snakemake interoperability.

Molecular Featurization Hub

K-Dense-AI/claude-scientific-skills

Molfeat is a Python toolkit that converts SMILES/RDKit molecules into embeddings via 100+ calculators, transformers, and pretrained models for QSAR, screening, similarity search, and deep learning pipelines.

Academic Paper Transformations

K-Dense-AI/claude-scientific-skills

Transforms LaTeX or PDF papers into interactive websites, narrated videos, and print-ready posters via the Paper2All pipeline, ideal for conference preparation, research promotion, and explorable academic showcases.

PDB Structure Explorer

K-Dense-AI/claude-scientific-skills

Access RCSB PDB to search biomolecular structures via text, sequence, or geometry queries, download coordinate files in PDB/mmCIF/Binary formats, retrieve metadata, and batch-process entries for drug discovery, protein engineering, and structural biology pipelines.

Polars Fast DataFrame

K-Dense-AI/claude-scientific-skills

Polars is a blazing fast in-memory DataFrame library based on Apache Arrow that replaces pandas for 1-100GB workloads, offering expression-based lazy execution, parallel operators, and rich I/O for ETL pipelines.

PyDESeq2 Differential Analysis

K-Dense-AI/claude-scientific-skills

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

Healthcare AI Toolkit

K-Dense-AI/claude-scientific-skills

PyHealth delivers a full-stack Python toolkit for building, evaluating, and deploying clinical machine learning models, covering EHR datasets, medical coding systems, physiological signals, and healthcare-tailored architectures such as RETAIN, SafeDrug, and Transformer-based pipelines.

PyOpenMS Mass Spectrometry

K-Dense-AI/claude-scientific-skills

PyOpenMS provides Python bindings for OpenMS to drive complete mass spectrometry workflows, covering data IO, spectral processing, feature/peptide-protein identification, quantitation, and metabolomics pipelines.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

Cloud Molecular Modeling Workflows

K-Dense-AI/claude-scientific-skills

Cloud-native Rowan orchestrates medicinal chemistry and molecular modeling pipelines via a Python API, offering pKa prediction, docking, descriptors, dynamics, and AI-driven structure workflows for scalable batch screening without local HPC.

Scanpy Single-Cell Pipeline

K-Dense-AI/claude-scientific-skills

Scanpy provides a scalable Python pipeline for single-cell RNA-seq, covering QC, normalization, dimensionality reduction, clustering, marker discovery, annotation, trajectory analysis, and publication-ready visualizations through AnnData.

Microbiome Bioinformatics Toolkit

K-Dense-AI/claude-scientific-skills

scikit-bio is a Python biological data toolkit for sequence handling, alignments, phylogenetic trees, microbial diversity metrics, and ecological stats, ideal for microbiome research pipelines that need FASTA/Newick I/O and ordination methods.

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