/ Recent content on Love, DNA & Code Hugo -- gohugo.io en Copyright © 2008–2025, Alfonso Saera plus the clarity & Hugo Authors Tue, 17 Mar 2026 00:00:00 +0000 /post/2026-03-17-openclaw/ Tue, 17 Mar 2026 00:00:00 +0000 /post/2026-03-17-openclaw/ How to install and configure OpenClaw in docker /post/2026-03-02-claudecodeskills/ Mon, 02 Mar 2026 00:00:00 +0000 /post/2026-03-02-claudecodeskills/ No more re-explaining your bioinformatics context to Claude. Skills embed domain expertise directly into Claude Code, eliminating repetitive setup and letting you focus on analysis questions. /post/2026-02-10-claude-nf-simpleaf/ Tue, 10 Feb 2026 00:00:00 +0000 /post/2026-02-10-claude-nf-simpleaf/ What happens when you ask an AI coding agent to build a complete scRNA-seq Nextflow pipeline from scratch? I put Claude Code to the test and share the results, the struggles, and the takeaways. /post/2026-02-04-claudecode/ Wed, 04 Feb 2026 00:00:00 +0000 /post/2026-02-04-claudecode/ Stop switching between IDEs and chat interfaces. Learn to delegate bioinformatics coding tasks directly from your terminal with Claude Code and focus on science, not syntax. /post/2025-09-10-matrix-mult/ Thu, 29 Jan 2026 00:00:00 +0000 /post/2025-09-10-matrix-mult/ From RNA-seq analysis to deep learning models Matrix multiplication is the heart of all bioinformatics computations. /post/2025-12-10-autoencoders/ Mon, 05 Jan 2026 00:00:00 +0000 /post/2025-12-10-autoencoders/ Explore the use of autoencoders to compress gene expression data and improve data analysis and visualization. /post/2025-11-25-biocpy/ Tue, 25 Nov 2025 00:00:00 +0000 /post/2025-11-25-biocpy/ A quick tour of biocpy, the first Python framework to deliver Bioconductor-style data structures and workflows for genomic data analysis. /post/2025-11-23-python-ggplot-tidyverse/ Sun, 23 Nov 2025 00:00:00 +0000 /post/2025-11-23-python-ggplot-tidyverse/ Learn how to implement a tidy and expressive R-like data analysis pipeline in Python, complete with dplyr-style transformations and ggplot-style plots. /post/2025-10-14-uv/ Tue, 14 Oct 2025 00:00:00 +0000 /post/2025-10-14-uv/ Replace pip & virtualenvwrapper with uv for instant, reproducible Python environments. /post/2025-08-31-nf4/ Sun, 31 Aug 2025 00:00:00 +0000 /post/2025-08-31-nf4/ Learn how to build bioinformatics pipelines with Nextflow, a powerful workflow management system for reproducible and scalable data analysis. PART 4 - Polish your pipeline /post/2025-08-30-nf3/ Sat, 30 Aug 2025 00:00:00 +0000 /post/2025-08-30-nf3/ Learn how to build bioinformatics pipelines with Nextflow, a powerful workflow management system for reproducible and scalable data analysis. PART 3 - Modularization & Configurable settings /post/2025-08-27-nf2/ Wed, 27 Aug 2025 00:00:00 +0000 /post/2025-08-27-nf2/ Learn how to build bioinformatics pipelines with Nextflow, a powerful workflow management system for reproducible and scalable data analysis. PART 2 - Multiple Samples /post/2025-08-06-alevinfry-vs-cellranger/ Wed, 06 Aug 2025 00:00:00 +0000 /post/2025-08-06-alevinfry-vs-cellranger/ Compare Alevin-fry’s pseudoalignment and Cell Ranger’s full alignment to find the right single-cell RNA-seq tool for your pipeline. /post/2025-07-30-nf1/ Wed, 30 Jul 2025 00:00:00 +0000 /post/2025-07-30-nf1/ Learn how to build bioinformatics pipelines with Nextflow, a powerful workflow management system for reproducible and scalable data analysis. /post/2025-07-28-alevinfry/ Mon, 28 Jul 2025 00:00:00 +0000 /post/2025-07-28-alevinfry/ Alevin-fry: pseudoalignment for computationally eficient single cell RNA-seq quantification /post/2025-06-05-pacmap/ Thu, 05 Jun 2025 00:00:00 +0000 /post/2025-06-05-pacmap/ Dimensional Reduction for Single Cell new player: PaCMAP /post/2025-05-25-single-cell-dimensional-phate/ Sun, 25 May 2025 00:00:00 +0000 /post/2025-05-25-single-cell-dimensional-phate/ There is more than just tSNE and UMAP in Single Cell Dimensional Reduction. In this post I will check Phate. /post/2025-05-16-tsne-umap/ Fri, 16 May 2025 00:00:00 +0000 /post/2025-05-16-tsne-umap/ t-SNE & UMAP dimensional reduction for single cell data. How to choose between them? /post/2025-04-29-trajectory-vsrnavelocity/ Tue, 13 May 2025 00:00:00 +0000 /post/2025-04-29-trajectory-vsrnavelocity/ Pseudotime trajectories and RNA velocity are computational approaches to analyze single cell dynamical process but, do they tell the same history? /post/2025-04-28-rnavelocity/ Mon, 28 Apr 2025 00:00:00 +0000 /post/2025-04-28-rnavelocity/ How to use scVelo to explore gene expression dynamics and differentiation /post/2025-04-06-slingshot/ Thu, 24 Apr 2025 00:00:00 +0000 /post/2025-04-06-slingshot/ Using Slingshot to calculate single cell trajectories /post/2025-02-17-pca/ Wed, 16 Apr 2025 00:00:00 +0000 /post/2025-02-17-pca/ PCA is the first step of single cell data analysis, but how many PCs should you use? /post/2025-04-01-enact/ Wed, 09 Apr 2025 00:00:00 +0000 /post/2025-04-01-enact/ See ENACT, a complete end-to-end pipeline that includes Visium HD Cell Segmentation and Cell type annotation, in action. /post/2025-03-22-bin2cell/ Wed, 26 Mar 2025 00:00:00 +0000 /post/2025-03-22-bin2cell/ Moving beyond nuclei segmentation, this post explores Bin2Cell for full cell segmentation in Visium HD spatial data. /post/2025-02-13-tensorflow/ Sat, 22 Mar 2025 00:00:00 +0000 /post/2025-02-13-tensorflow/ Easiest way to install and use TensorFlow /post/2025-01-17-visiumhd-segmentation/ Wed, 19 Mar 2025 00:00:00 +0000 /post/2025-01-17-visiumhd-segmentation/ Nuclei segmentation from Visium HD data /post/2025-01-26-sce/ Thu, 13 Mar 2025 00:00:00 +0000 /post/2025-01-26-sce/ Explore SingleCellExperiment in R! Master data structures & workflows to handle single-cell RNA-seq data effectively in your research projects. /post/2025-02-02-seurat/ Thu, 06 Mar 2025 00:00:00 +0000 /post/2025-02-02-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. /post/2025-01-31-anndata-and-scanpy-basics/ Thu, 27 Feb 2025 00:00:00 +0000 /post/2025-01-31-anndata-and-scanpy-basics/ Unlock the power of Scanpy! Discover how to efficiently store and manage single-cell RNA-seq data using AnnData in Python. /post/2025-01-15-chatgpt/ Thu, 20 Feb 2025 00:00:00 +0000 /post/2025-01-15-chatgpt/ This post will show you how to use LLM AI tools to write code for you.