đź““ Welcome to my Bioinformatics Notebook

Notebook: 08-01-2025

LinkedIn Email


Hi there đź‘‹

I hope you’re doing well, and that you find these notes useful for your analysis.

You probably landed here because you’re:

  • looking for a quick overview for single cell
  • searching for considerations when running downstream analysis, or
  • simply exploring out of curiosity

Whatever the reason, welcome 🙌

This space is a collection of my working notes on single-cell RNA-seq, multiome (snRNA-seq + snATAC-seq), and Visium Spatial Transcriptomics. It’s a work in progress and not meant to be a full start-to-finish guide for replicating pipelines, there are already a lot of reds of excellent resources out there, many far more comprehensive than I could write. Plus, each project comes with its own technical quirks and biological context. Most of my real solutions are pieced together from a mix of solid references and adapted to fit the specific problems at hand.

Instead, my aim here is to share the kind of material I often find relevant, missed or scattered: notes that go beyond tutorials which are some times too simplified or too narrow (tied to a single research context). These entries are intended as practical, high-level references with sketches, conceptual maps, and notes that help me (and hopefully you) connect the dots more clearly.

I’m always happy to connect! If you’d like to swap workflows, brainstorm methods, or talk about new opportunities, feel free to reach out.

What you’ll find here


Concise, high-level notes, often illustrated with videos, conceptual maps, sketches, or visualizations to highlight specific analyses (Section I).

In addition, you’ll find technical support notes organized into five main areas (Section II):

  • Key Literature – I value a lot published work, so papers are used to refer cases that provide essential context
  • Vignettes & Tutorials – broad but practical guides
  • Core Functions & References – relevant functions and documentation
  • Custom Repo Practices – workflow tips from real projects found on the network
  • Behind-the-Scenes Tools & File Formats – underrated but essential resources

Why share this?


Have you ask yourself … “why on earth did I think that would work?” moments. By sharing my notes, I hope to reach any of the following goals:

  • Help others dodge some of the same pitfalls (My friend. You are not alone!) At least feel less alone while falling it, every one started with a single line
  • Gather links to papers, vignettes, blog posts, Twitter threads, and other resources that have shaped my work (and probably saved me from disaster more than once)
  • Show the kind of experience (and occasional stubbornness) it takes to get from raw data to conclusions
  • Build a transparent portfolio of how I think through data

💡 If you spot mistakes, have suggestions, or just want to geek out about data, your feedback is very welcome. I’m always tweaking things here to make it more useful, for myself and hopefully for others, and if you’d like to reach out directly, feel free to use the contact info in my contact data above (LinkedIn or email).

Have a wonderful day 🌱🧠
Cynthia S. Cardinault