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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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  • Single cell in R: Seurat

    calendar Mar 6, 2025 · 1614 min read · single cell Seurat RNAseq code  ·
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    Single cell in R: Seurat

    Get started with Seurat, the Satija's lab R package for single-cell analysis. This beginner-friendly guide covers object's structure and essential functions.


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  • Single cell in Python: Scanpy and AnnData

    calendar Feb 27, 2025 · 8 min read · single cell code  ·
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    Single cell in Python: Scanpy and AnnData

    Unlock the power of Scanpy! Discover how to efficiently store and manage single-cell RNA-seq data using AnnData in Python.


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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

  • Find Marker Genes Using Effect Size
  • Skills: Teach Claude Code Bioinformatics
  • 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

Recent Posts

  • OpenClaw Setup
  • 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

Categories

BIOINFORMATICS 23 R 13 PYTHON 12 CODE 6 TECHNOLOGY 6 NEXTFLOW 5 BIONFORMATICS 1 OPENCLAW 1

Tags

CODE 22 SINGLE CELL 20 RNASEQ 11 AI 8 BIOCONDUCTOR 6 DEEP LEARNING 5 DIMENSIONAL REDUCTION 4 PSEUDOALIGNMENT 4 CELL SEGMENTATION 3 CLAUDE 3 LLM 3 PSEUDOTIME 3 PYTHON 3 SPATIAL 3
All Tags
AGENT1 AI8 BIOCONDUCTOR6 CELL ANNOTATION1 CELL SEGMENTATION3 CHATGPT1 CLAUDE3 CODE22 COHEN'S D1 DEEP LEARNING5 DIFFERENTIAL EXPRESSION ANALYSIS1 DIMENSIONAL REDUCTION4 INDEX1 LLM3 MARKER GENES1 OPENCLAW1 P-VALUE1 PHATE1 PLOTS2 PRODUCTIVITY1 PSEUDOALIGNMENT4 PSEUDOTIME3 PYTHON3 RNA VELOCITY2 RNASEQ11 SCANPY1 SCVELO1 SEURAT1 SINGLE CELL20 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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