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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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  • Understanding Cellular Dynamics with RNA Velocity

    calendar Apr 28, 2025 · 7 min read · RNA velocity scVelo scanpy Pseudotime single cell RNAseq  ·
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    Understanding Cellular Dynamics with RNA Velocity

    How to use scVelo to explore gene expression dynamics and differentiation


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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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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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