Love, DNA & Code

Use uv and forget about virtualenvwrapper

Oct 14, 2025 · 5 min read · uv ·
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Replace pip & virtualenvwrapper with uv for instant, reproducible Python environments.

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

Aug 31, 2025 · 8 min read · code single cell pseudoalignment RNAseq ·
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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

Aug 30, 2025 · 5 min read · code single cell pseudoalignment RNAseq ·
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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

Aug 27, 2025 · 9 min read · code single cell pseudoalignment RNAseq ·
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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

Aug 6, 2025 · 9 min read · Bioconductor code single cell RNAseq ·
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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

Jul 30, 2025 · 8 min read · code single cell pseudoalignment RNAseq ·
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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

Jul 28, 2025 · 4 min read · code single cell ·
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Alevin-fry: pseudoalignment for computationally eficient single cell RNA-seq quantification

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Pairwise Controlled Manifold Approximation (PaCMAP) for Single Cell

Jun 5, 2025 · 21 min read · dimensional reduction code single cell ·
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Dimensional Reduction for Single Cell new player: PaCMAP

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Single Cell Dimensional Reduction: Phate

May 25, 2025 · 22 min read · code single cell dimensional reduction phate ·
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There is more than just tSNE and UMAP in Single Cell Dimensional Reduction. In this post I will check Phate.

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Single Cell Dimensional Reduction: t-SNE vs UMAP

May 16, 2025 · 11 min read · code single cell dimensional reduction t-SNE UMAP ·
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t-SNE & UMAP dimensional reduction for single cell data. How to choose between them?

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