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Genomic Interval Embeddings

K-Dense-AI/scientific-agent-skills

Geniml builds machine learning workflows around BED and scATAC datasets to learn embeddings for regions, metadata, and cells, enabling similarity searches, clustering, consensus peaks, and downstream analysis of genomic intervals.

Genomic Interval Toolkit

K-Dense-AI/scientific-agent-skills

High-performance Rust toolkit with Python bindings for genomic interval analysis, covering overlap detection, coverage track generation, ML tokenization, reference sequence handling, fragment processing, and scoring workflows for sequencing datasets.

Molecular Featurization Hub

K-Dense-AI/scientific-agent-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.

Hardware-Agnostic Quantum ML

K-Dense-AI/scientific-agent-skills

Hardware-agnostic quantum ML framework enabling gradient-based training of quantum circuits, hybrid quantum-classical models, and seamless integration with PyTorch/JAX/TensorFlow alongside device portability across IBM/Google/Rigetti/IonQ.

PyDESeq2 Differential Analysis

K-Dense-AI/scientific-agent-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.

PyOpenMS Mass Spectrometry

K-Dense-AI/scientific-agent-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/scientific-agent-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.

Intelligent Research Information Lookup

research-lookup

K-Dense-AI/scientific-agent-skills

This skill provides intelligent, multi-backend research lookup, automatically routing queries to the optimal source. It utilizes fast web search for general queries, the Parallel Chat API for deep synthesis, and Perplexity for academic paper searches. Use it to gather up-to-date scientific findings, verify facts, analyze market trends, or retrieve technical documentation.

Scholar Evaluation Framework

scholar-evaluation

K-Dense-AI/scientific-agent-skills

This skill runs the ScholarEval framework to score academic submissions across problem setting, methodology, data, analysis, writing, and references, providing structured strengths/weaknesses, numeric ratings, and guidance for visualizing the evaluation.

Fast UMAP Dimensionality Reduction

K-Dense-AI/scientific-agent-skills

Use UMAP for fast nonlinear manifold reduction to produce embeddings that keep local and global structure, making it ideal for visualization, clustering preprocessing, supervised/parametric workflows, or high-dimensional feature engineering.

US Treasury Fiscal API

K-Dense-AI/scientific-agent-skills

Provides open REST access to the U.S. Treasury Fiscal Data API so analysts can pull national debt, spending, revenue, interest rates, exchange rates, auctions, and savings bond statistics without an API key; useful for financial dashboards, debt tracking, and research involving federal fiscal metrics.

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