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  • From Prompt to Pipeline: Building a scRNA-seq Workflow with Claude Code and Nextflow

    calendar Feb 10, 2026 · 9 min read · AI Deep Learning LLM Code Claude single cell RNAseq  ·
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    From Prompt to Pipeline: Building a scRNA-seq Workflow with Claude Code and Nextflow

    What happens when you ask an AI coding agent to build a complete scRNA-seq Nextflow pipeline from scratch? I put Claude Code to the test and share the results, the struggles, and the takeaways.


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  • Claude Code for Bioinformaticians: Your AI Coding Assistant in the Terminal

    calendar Feb 4, 2026 · 14 min read · AI Deep Learning LLM Code Claude  ·
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    Claude Code for Bioinformaticians: Your AI Coding Assistant in the Terminal

    Stop switching between IDEs and chat interfaces. Learn to delegate bioinformatics coding tasks directly from your terminal with Claude Code and focus on science, not syntax.


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  • Performing Exploratory analysis without writing a line of code

    calendar Feb 20, 2025 · 7 min read · AI ChatGPT code LLM Plots  ·
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    Performing Exploratory analysis without writing a line of code

    This post will show you how to use LLM AI tools to write code for you.


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Alfonso Saera Vila

Welcome to 'Love, DNA & Code' my blog about new bioinformatics tools, single-cell & spatial applications, AI, and more.
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Featured Posts

  • From Prompt to Pipeline: Building a scRNA-seq Workflow with Claude Code and Nextflow
  • Claude Code for Bioinformaticians: Your AI Coding Assistant in the Terminal
  • BiocPy: Bioconductor in Python
  • Building Your First Nextflow Pipeline: PART 4 - Polish your pipeline
  • Single Cell Dimensional Reduction: t-SNE vs UMAP
  • Pseudotime Trajectory vs RNA Velocity
  • Single Cell PCA Deep Dive
  • Visium HD cell segmentation with Bin2Cell

Recent Posts

  • The Basics of Matrix Multiplication
  • Autoencoders for Single Cell Data Analysis
  • Bringing the Tidyverse to Python: plotnine, siuba, and pyjanitor
  • Use uv for python and forget about anything else!
  • Building Your First Nextflow Pipeline: PART 3 - Modularization & Configurable settings
  • Building Your First Nextflow Pipeline: PART 2 - Multiple Samples
  • Alignment or Pseudoalignment: Alevin-fry vs Cell Ranger comparison
  • Building Your First Nextflow Pipeline: PART 1 - One sample at a time

Categories

BIOINFORMATICS 22 PYTHON 12 R 12 NEXTFLOW 5 TECHNOLOGY 5 CODE 4 BIONFORMATICS 1

Tags

CODE 20 SINGLE CELL 19 RNASEQ 11 AI 6 BIOCONDUCTOR 6 DEEP LEARNING 5 DIMENSIONAL REDUCTION 4 PSEUDOALIGNMENT 4 CELL SEGMENTATION 3 LLM 3 PSEUDOTIME 3 PYTHON 3 SPATIAL 3 CLAUDE 2
All Tags
AI6 BIOCONDUCTOR6 CELL ANNOTATION1 CELL SEGMENTATION3 CHATGPT1 CLAUDE2 CODE20 DEEP LEARNING5 DIMENSIONAL REDUCTION4 INDEX1 LLM3 PHATE1 PLOTS2 PSEUDOALIGNMENT4 PSEUDOTIME3 PYTHON3 RNA VELOCITY2 RNASEQ11 SCANPY1 SCVELO1 SEURAT1 SINGLE CELL19 SPATIAL3 T-SNE1 TENSORFLOW1 TRAJECTORY ANALYSIS2 UMAP1 UV1
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Copyright © 2008–2025, Alfonso Saera plus the clarity & Hugo Authors

Copyright  COPYRIGHT © 2008–2025, ALFONSO SAERA PLUS THE CLARITY & HUGO AUTHORS. All Rights Reserved

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