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Matt Paul

@sciencematt.bsky.social
231 followers 1K following 5 posts

Bioinformatics Analyst at Rockefeller University Working on all the fun genomics | Training and Reproducibility Lead Developer of Bioconductor package Herper for managing conda in R www.bioconductor.org/packages/relea…

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Reposted by Matt Paul
Joachim Goedhart @joachimgoedhart.bsky.social · 16/12/2024
There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...
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Reposted by Matt Paul
Claus Wilke @clauswilke.com · 06/12/2024
This is a good recommendation. In addition, for bar plots or other plots where you're coloring large areas, add some transparency. The viridis colors are too dark and saturated for large areas. They were designed for points and lines(*). Compare left versus right.
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Reposted by Matt Paul
Fabio Crameri @fabiocrameri.ch · 05/10/2023
Scientific colour maps 8.0 · Perceptually uniform · Perceptually ordered · Colour-blind friendly · Readable as B&W print · Widely compatible · Versioned & citable fabiocrameri.ch/colourmaps #useBatlow #Dataviz #SciArt #EduSky #OpenSource 1/n
Entire suite of Scientific colour maps (perceptually uniform and color-blind friendly) by Fabio Crameri, with hand-pickable colours of discrete and categorical colour palettes.
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Reposted by Matt Paul
Dichromat Chloe (4% of scientists) @dichromat-chloe.bsky.social · 25/11/2024
(please amplify) 4% of scientists face an important barrier to an the ENTIRE FIELD of single-cell genomics and here is why
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Reposted by Matt Paul
James Bartlett @bartlettje.bsky.social · 22/11/2024
I've added a little code peer-review activity for the final week of my introductory research methods course. I came across this great concise article which outlines what elements to include for code-review in the sciences: onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com
Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology
Code review is the process of either informally (as part of a group, as colleagues) or formally (as part of the peer review process) checking and evaluating each other's code and is a critical method...
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Reposted by Matt Paul
Frank Harrell @f2harrell.bsky.social · 22/11/2024
Really nice addition to #RStats ggplot2 graphics
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Reposted by Matt Paul
Vincent Arel-Bundock @vincentab.bsky.social · 21/11/2024
𝚝𝚒𝚗𝚢𝚝𝚊𝚋𝚕𝚎 0.6.1 for #Rstats is out! It's an ultra simple, super flexible, and 0-dependency package to draw beautiful tables in HTML, LaTeX, Typst, Word, PDF, and PNG. And for those who ❤️ documentation, 𝚝𝚒𝚗𝚢𝚝𝚊𝚋𝚕𝚎 ships with a billion pages of tutorials: vincentarelbundock.github.io/tinytable/
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Reposted by Matt Paul
Lior Pachter @lpachter.bsky.social · 21/11/2024
You can now run tximport in Python with pytximport thanks to @compmed.bsky.social et al. academic.oup.com/bioinformati...
academic.oup.com
Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python
AbstractSummary. Transcript quantification tools efficiently map bulk RNA sequencing reads to reference transcriptomes. However, their output consists of t
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Reposted by Matt Paul
Colin 🤘🌱🏃‍♀️ @colinfay.bsky.social · 19/11/2024
#RStats I'm so happy to finally share what we've been experimenting on at ThinkR for the past couple of weeks — A native mobile app that can run R code through #webR Read more at 👉 rtask.thinkr.fr/youve-been-w...
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Matt Paul @sciencematt.bsky.social · 18/11/2024
Lots of good bioinformatics starter packs. Many of the starter packs I used last week have already been updated as the influx continues.
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Matt Paul @sciencematt.bsky.social · 16/11/2024
Super useful guide by @jacoates.bsky.social for understanding some of the new quirks (and benefits) of BlueSky. Feels like the Starter Packs have been a great way to get me going, but I'm going to need some custom feeds to parse all these new people I'm following!
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