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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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  • Pseudotime Trajectory vs RNA Velocity

    calendar May 13, 2025 · 14 min read · code Pseudotime single cell RNA velocity Trajectory analysis Bioconductor  ·
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    Pseudotime Trajectory vs RNA Velocity

    Pseudotime trajectories and RNA velocity are computational approaches to analyze single cell dynamical process but, do they tell the same history?


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  • Pseudotime Trajectories with Slingshot

    calendar Apr 24, 2025 · 12 min read · code Trajectory analysis Pseudotime single cell RNAseq Bioconductor  ·
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    Pseudotime Trajectories with Slingshot

    Using Slingshot to calculate single cell trajectories


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  • Single Cell PCA Deep Dive

    calendar Apr 16, 2025 · 7 min read · single cell code Bioconductor  ·
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    Single Cell PCA Deep Dive

    PCA is the first step of single cell data analysis, but how many PCs should you use?


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  • Single cell Bioconductor's choice: SCE

    calendar Mar 13, 2025 · 19 min read · single cell Bioconductor RNAseq code  ·
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    Single cell Bioconductor's choice: SCE

    Explore SingleCellExperiment in R! Master data structures & workflows to handle single-cell RNA-seq data effectively in your research projects.


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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

  • Building Your First Nextflow Pipeline: PART 4 - Polish your pipeline
  • 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
  • Pseudoalignment for single cell RNA-seq with alevin-fry
  • Pairwise Controlled Manifold Approximation (PaCMAP) for Single Cell
  • Single Cell Dimensional Reduction: Phate

Categories

BIOINFORMATICS 19 R 10 PYTHON 6 TECHNOLOGY 5 NEXTFLOW 4

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Copyright © 2008–2025, Alfonso Saera plus the clarity & Hugo Authors

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