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Spark Job Optimization and Tuning

spark-optimization

sickn33/antigravity-awesome-skills

This guide provides advanced patterns and best practices for optimizing Apache Spark jobs. It covers critical areas like effective partitioning, memory tuning, minimizing data skew, and optimizing different types of joins (broadcast, bucket). Use this when troubleshooting slow, large-scale data processing workflows or needing to scale Spark pipelines efficiently and reliably.

Spark Sql Optimizer

spark-sql-optimizer

jeremylongshore/claude-code-plugins-plus-skills

Automates Spark SQL optimizer tasks in data pipelines by guiding best practices, producing production-ready code and configurations, and validating ETL, transformation, orchestration, and streaming workflows.

SQL Transform Helper

sql-transform-helper

jeremylongshore/claude-code-plugins-plus-skills

Automated guidance for SQL transform helper tasks within data pipelines, covering ETL, data transformation, workflow orchestration, and streaming, while following best practices, generating production-ready code, and validating results.

Advanced GPU Performance Tuning for AI

vastai-performance-tuning

jeremylongshore/claude-code-plugins-plus-skills

A comprehensive guide to optimizing deep learning workflows and maximizing efficiency on cloud GPU platforms like Vast.ai. Learn techniques for selecting optimal instances by performance-per-dollar, reducing startup latency, tuning data pipelines (DataLoader, pin_memory), and scaling multi-GPU training using PyTorch and Bash scripting.

COSMIC Mutation Access

cosmic-database

K-Dense-AI/claude-scientific-skills

Programmatic access to the COSMIC cancer mutation database for downloading mutations, Cancer Gene Census, mutational signatures, fusions, copy number, expression, and resistance data to fuel oncology research or bioinformatics pipelines after authentication.

DNAnexus Cloud Genomics

dnanexus-integration

K-Dense-AI/claude-scientific-skills

Integrate with the DNAnexus cloud genomics platform to build apps/applets, manage FASTQ/BAM/VCF data, run workflows, and script automations via dxpy for biomedical pipelines.

ENA Sequence Access

K-Dense-AI/claude-scientific-skills

Access the European Nucleotide Archive via REST/FTP to fetch DNA/RNA sequences, raw reads, assemblies, annotations, and taxonomy for research or bioinformatics pipelines.

Ensembl Genome API

ensembl-database

K-Dense-AI/claude-scientific-skills

Query Ensembl’s RESTful API to access gene annotations, sequences, variants, orthologs, and assembly mappings across 250+ species, enabling integration into genomic research pipelines.

FlowIO FCS Handler

K-Dense-AI/claude-scientific-skills

FlowIO reads and writes Flow Cytometry Standard (FCS) files, exposing metadata, channels, and NumPy event arrays while allowing CSV/DataFrame conversion, making it ideal for cytometry pipelines and backend preprocessing services.

NCBI Gene Explorer

K-Dense-AI/claude-scientific-skills

Access NCBI Gene data via E-utilities or Datasets API to look up genes by symbol or ID, retrieve RefSeqs, GO terms, chromosomal locations, phenotypes, and run batch workflows for annotation pipelines.

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.

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.

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