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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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  • 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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  • Single Cell Dimensional Reduction: Phate

    calendar May 25, 2025 · 22 min read · code single cell dimensional reduction phate  ·
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    Single Cell Dimensional Reduction: Phate

    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

    calendar May 16, 2025 · 11 min read · code single cell dimensional reduction t-SNE UMAP  ·
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    Single Cell Dimensional Reduction: t-SNE vs UMAP

    t-SNE & UMAP dimensional reduction for single cell data. How to choose between them?


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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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