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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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  • 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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  • Building Your First Nextflow Pipeline: PART 1 - One sample at a time

    calendar Jul 30, 2025 · 8 min read · code single cell pseudoalignment RNAseq  ·
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    Building Your First Nextflow Pipeline: PART 1 - One sample at a time

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


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  • Pseudoalignment for single cell RNA-seq with alevin-fry

    calendar Jul 28, 2025 · 4 min read · code single cell  ·
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    Pseudoalignment for single cell RNA-seq with alevin-fry

    Alevin-fry: pseudoalignment for computationally eficient single cell RNA-seq quantification


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  • Pairwise Controlled Manifold Approximation (PaCMAP) for Single Cell

    calendar Jun 5, 2025 · 21 min read · dimensional reduction code single cell  ·
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    Pairwise Controlled Manifold Approximation (PaCMAP) for Single Cell

    Dimensional Reduction for Single Cell new player: PaCMAP


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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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