Matt Paul
@sciencematt.bsky.social
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
https://www.bioconductor.org/packages/release/bioc/html/Herper.html
Working on all the fun genomics | Training and Reproducibility
Lead Developer of Bioconductor package Herper for managing conda in R
https://www.bioconductor.org/packages/release/bioc/html/Herper.html
Reposted by Matt Paul
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...
December 16, 2024 at 9:25 AM
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...
Reposted by Matt Paul
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.
Compare left versus right.
December 6, 2024 at 8:54 PM
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.
Compare left versus right.
Reposted by Matt Paul
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
· 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
October 5, 2023 at 1:15 PM
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
· 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
Reposted by Matt Paul
(please amplify) 4% of scientists face an important barrier to an the ENTIRE FIELD of single-cell genomics and here is why
November 25, 2024 at 3:22 PM
(please amplify) 4% of scientists face an important barrier to an the ENTIRE FIELD of single-cell genomics and here is why
Reposted by Matt Paul
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....
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...
onlinelibrary.wiley.com
November 22, 2024 at 4:36 PM
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....
Reposted by Matt Paul
Really nice addition to #RStats ggplot2 graphics
The brand new `legendry` package by @teunbrand.bsky.social takes ggplots2 guides to the next level 🤩
teunbrand.github.io/teunbrand_bl...
teunbrand.github.io/teunbrand_bl...
November 22, 2024 at 12:30 PM
Really nice addition to #RStats ggplot2 graphics
Reposted by Matt Paul
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/
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/
November 21, 2024 at 2:38 PM
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/
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/
Reposted by Matt Paul
You can now run tximport in Python with pytximport thanks to @compmed.bsky.social et al. academic.oup.com/bioinformati...
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
academic.oup.com
November 21, 2024 at 12:19 AM
You can now run tximport in Python with pytximport thanks to @compmed.bsky.social et al. academic.oup.com/bioinformati...
Reposted by Matt Paul
#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...
Read more at 👉 rtask.thinkr.fr/youve-been-w...
November 19, 2024 at 12:44 PM
#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...
Read more at 👉 rtask.thinkr.fr/youve-been-w...
Lots of good bioinformatics starter packs. Many of the starter packs I used last week have already been updated as the influx continues.
For anyone joining, @stephenturner.us has an awesome post for getting set up here. And welcome, let's keep the good vibes going! blog.stephenturner.us/p/bluesky-fo...
Bluesky for Science
Bluesky starter packs for genomics, bioinformatics, R, and Nextflow
blog.stephenturner.us
November 18, 2024 at 7:25 PM
Lots of good bioinformatics starter packs. Many of the starter packs I used last week have already been updated as the influx continues.
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!
New to @bsky.app?
Here's a quick getting started guide, primarily aimed at scientists zenodo.org/records/1414...
#AcademicSky
Here's a quick getting started guide, primarily aimed at scientists zenodo.org/records/1414...
#AcademicSky
Getting started on BlueSky; a guide for scientists
A quick getting started guide for using BlueSky, aimed primarily at scientists, particularly those interested in open science and research culture
zenodo.org
November 16, 2024 at 3:41 PM
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!