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

    calendar Feb 4, 2026 · 13 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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  • The Basics of Matrix Multiplication

    calendar Jan 29, 2026 · 5 min read · code Deep Learning AI  ·
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    The Basics of Matrix Multiplication

    From RNA-seq analysis to deep learning models Matrix multiplication is the heart of all bioinformatics computations.


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  • Autoencoders for Single Cell Data Analysis

    calendar Jan 5, 2026 · 48 min read · AI Deep Learning dimensional reduction single cell RNAseq  ·
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    Autoencoders for Single Cell Data Analysis

    Explore the use of autoencoders to compress gene expression data and improve data analysis and visualization.


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  • BiocPy: Bioconductor in Python

    calendar Nov 25, 2025 · 8 min read · Bioconductor single cell  ·
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    BiocPy: Bioconductor in Python

    A quick tour of biocpy, the first Python framework to deliver Bioconductor-style data structures and workflows for genomic data analysis.


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  • Bringing the Tidyverse to Python: plotnine, siuba, and pyjanitor

    calendar Nov 23, 2025 · 7 min read · code Plots  ·
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    Bringing the Tidyverse to Python: plotnine, siuba, and pyjanitor

    Learn how to implement a tidy and expressive R-like data analysis pipeline in Python, complete with dplyr-style transformations and ggplot-style plots.


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  • Use uv for python and forget about anything else!

    calendar Oct 14, 2025 · 5 min read · uv  ·
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    Use uv for python and forget about anything else!

    Replace pip & virtualenvwrapper with uv for instant, reproducible Python environments.


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  • Building Your First Nextflow Pipeline: PART 4 - Polish your pipeline

    calendar Aug 31, 2025 · 8 min read · code single cell pseudoalignment RNAseq  ·
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    Building Your First Nextflow Pipeline: PART 4 - Polish your pipeline

    Learn how to build bioinformatics pipelines with Nextflow, a powerful workflow management system for reproducible and scalable data analysis. PART 4 - Polish your pipeline


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  • Building Your First Nextflow Pipeline: PART 3 - Modularization & Configurable settings

    calendar Aug 30, 2025 · 5 min read · code single cell pseudoalignment RNAseq  ·
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    Building Your First Nextflow Pipeline: PART 3 - Modularization & Configurable settings

    Learn how to build bioinformatics pipelines with Nextflow, a powerful workflow management system for reproducible and scalable data analysis. PART 3 - Modularization & Configurable settings


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  • Building Your First Nextflow Pipeline: PART 2 - Multiple Samples

    calendar Aug 27, 2025 · 9 min read · code single cell pseudoalignment RNAseq  ·
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    Building Your First Nextflow Pipeline: PART 2 - Multiple Samples

    Learn how to build bioinformatics pipelines with Nextflow, a powerful workflow management system for reproducible and scalable data analysis. PART 2 - Multiple Samples


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  • Alignment or Pseudoalignment: Alevin-fry vs Cell Ranger comparison

    calendar Aug 6, 2025 · 9 min read · Bioconductor code single cell RNAseq  ·
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    Alignment or Pseudoalignment: Alevin-fry vs Cell Ranger comparison

    Compare Alevin-fry’s pseudoalignment and Cell Ranger’s full alignment to find the right single-cell RNA-seq tool for your pipeline.


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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

  • Visium HD cell segmentation with Bin2Cell
  • Single cell in Python: Scanpy and AnnData

Recent Posts

  • Claude Code for Bioinformaticians: Your AI Coding Assistant in the Terminal
  • The Basics of Matrix Multiplication
  • Autoencoders for Single Cell Data Analysis
  • BiocPy: Bioconductor in Python
  • Bringing the Tidyverse to Python: plotnine, siuba, and pyjanitor
  • Use uv for python and forget about anything else!
  • Building Your First Nextflow Pipeline: PART 4 - Polish your pipeline
  • Building Your First Nextflow Pipeline: PART 3 - Modularization & Configurable settings

Categories

BIOINFORMATICS 22 R 12 PYTHON 11 TECHNOLOGY 5 NEXTFLOW 4 CODE 3

Tags

CODE 19 SINGLE CELL 18 RNASEQ 10 BIOCONDUCTOR 6 AI 5 DEEP LEARNING 4 DIMENSIONAL REDUCTION 4 PSEUDOALIGNMENT 4 CELL SEGMENTATION 3 PSEUDOTIME 3 PYTHON 3 SPATIAL 3 LLM 2 PLOTS 2
All Tags
AI5 BIOCONDUCTOR6 CELL ANNOTATION1 CELL SEGMENTATION3 CHATGPT1 CLAUDE1 CODE19 DEEP LEARNING4 DIMENSIONAL REDUCTION4 INDEX1 LLM2 PHATE1 PLOTS2 PSEUDOALIGNMENT4 PSEUDOTIME3 PYTHON3 RNA VELOCITY2 RNASEQ10 SCANPY1 SCVELO1 SEURAT1 SINGLE CELL18 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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