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Thomas Sandmann

@thomas-sandmann.genomic.social.ap.brid.gy
51 followers 8 following 38 posts

Computational biologist, biotech, neurodegeneration, genomics, learning, R, python [bridged from genomic.social/@thomas_sandmann on the fediverse by fed.brid.gy ]

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Thomas Sandmann @thomas-sandmann.genomic.social.ap.brid.gy · 14/10/2026
I am learning about recent methods for single-cell RNA-seq analysis. The open access review "**Representation learning of single-cell RNA-seq data**" by @const_ae, @janlause and colleagues is great! Very helpful to see so many methods positioned within clear […] [Original post on genomic.social]
Figure 2 by Constantin Ahlmann-Eltze, Florian Barkmann, Jan Lause, Valentina Boeva and Dmitry Kobak3: Conceptual illustrations of the four families of representation learning methods. (KL divergence) Kullback–Leibler divergence, (NB) negative binomial distribution, (ZINB) zero-inflated negative binomial distribution, (CLS) classification token.
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Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 01/10/2026
Oh, no! My R package {safespace} is in a broken state - won't someone (new to PRs) help me fix it??? I'm renewing my offer to guide newbies through the R package building / fixing / reviewing process during Hacktoberfest - see this post […]
fosstodon.org
Original post on fosstodon.org
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Reposted by Thomas Sandmann
Julia Evans @b0rk.social.jvns.ca.ap.brid.gy · 21/09/2026
Are you interested in learning how to use Git for the first time? (or almost the first time) we're looking for Git beginners to give us feedback on a Git tutorial! The tutorial will be open source when it's released, so you'll be helping many future beginners! Sign up here […]
social.jvns.ca
Original post on social.jvns.ca
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Reposted by Thomas Sandmann
Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 13/09/2026
Dear Bubble, the far right is on the rise - not just in Germany. But that a Nazi party won an election in a German country state, 80 years after WWII, made the headline in many papers. And it concerns many of you. I have many friends and acquaintances […] [Original post on fediscience.org]
Protest sign, quoting an AfD member who wants to found a new SA to "clean up" society.
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Pottery by Osa @potterybyosa.mastodon.social.ap.brid.gy · 08/09/2026
Last night, my husband took me to see "A Life Illuminated" about Dr. Edith Widder, the first marine biologist to document deep ocean #bioluminescence. To me, the #film served as a reminder to leave room in our minds for the beautiful, magical things that exist in this life that we don't often […]
mastodon.social
Original post on mastodon.social
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Reposted by Thomas Sandmann
vincentholst.bsky.social @vincentholst.bsky.social · 13/08/2026
In 2023, @nature.com published 'Papers and patents are becoming less disruptive over time', receiving world-wide media attention. Our Matters Arising, published after a 32 month delay (more on that soon), shows that the reported decline can largely be attributed to dataset artefacts. 🧵
The average CD_5 index per year for Web of Science. The original Park et al. decline (top curve) becomes essentially flat (bottom curve) when removing papers with CD_5=1. Those papers largely correspond to dataset artefacts.
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Niki @nikitonsky.mastodon.online.ap.brid.gy · 20/07/2026
I am looking for work! Clojure, or, maybe, something native, closer to the metal. RT for reach please 🙏 tonsky.me/blog/work-2026
tonsky.me
Looking for work
Hey, Niki here. This is a bit unusual. My sabbatical is coming to an end, and I am looking for a new opportunity. Full-time or contract, startup or research, remote or Berlin, individual contributor, ideally—tight team, ambitious product. I am a software engineer first and foremost with 20+ years of experience. I work on technically challenging products, foundational technology, dev tools. I’ve been doing Clojure and web recently, but I'm also very excited to explore closer-to-the-metal programming. I have an eye for design, user interfaces, UX, DX. I would love to work with a team that takes interface quality seriously. Or to work with graphics! I am pretty sure I am good at explaining stuff, including what we are building, why, why this way, why is it important, etc. For example. The overarching theme is to understand computers deeply, and then use that to make better and simpler software. If you care about that too, we might be a great match! # Recent work Instant DB is a US startup building a modern Firebase. I worked on the sync algorithm, performance, DX. A summary of my commit log. Roam Research is an OG personal knowledge manager. I worked on database optimization and a plugin system. At JetBrains, I developed a new Skia renderer for Fleet and Jetpack Compose Desktop. I’ve built many open-source libraries, including a database, a GUI toolkit, a Clojure dev environment, a React wrapper, a well-known font... More recently, Clojure+ gives you a taste of my approach to DX, and Fast EDN—to performance. I maintain several active projects — AlleKinos.de, Grumpy Website, this site. If you want to dive deeper, here’s the usual stuff: Projects / Talks / LinkedIn / GitHub # Why this post? It’s an attempt to reach beyond my immediate network. I’ve been doing Clojure for a long time, and now want to explore. If you are working on a compiler, a database, an IDE, a programming language or another technically ambitious product, touching graphics, typography, algorithms, low-level programming, and you think my experience can help, let’s talk: niki@tonsky.me.
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Stephen Turner @stephenturner.us · 15/07/2026
Ten quick tips to SNIFF out sustainable and secure scientific software journals.plos.org/ploscompbiol... 🧬💻🧪
journals.plos.org
Ten quick tips to SNIFF out sustainable and secure scientific software
Modern computational biology depends heavily on open-source software tools, analysis pipelines, and containerized workflows developed and shared by the research community. While there is extensive gui...
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Preston Maness ☭ @aspensmonster.tenforward.social.ap.brid.gy · 11/07/2026
And this bit in particular reminded me of Carl Sagan when he spoke about books in Cosmos: >Continuity is how a society talks to itself across time. It is how we remain connected to what we have done and what has been done for us. I can practically hear Sagan's voice: >What an astonishing […]
tenforward.social
Original post on tenforward.social
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Reposted by Thomas Sandmann
Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 07/07/2026
A long shot, but the local opportunities seem a bit thin at the moment. I'm available for hire if you're looking for #rstats package development, maintenance, translation, etc... Need some help implementing a solution? Want to productionise a script into a robust package? Wish a third-party […]
fosstodon.org
Original post on fosstodon.org
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Grant McDermott @gmcd.bsky.social · 03/07/2026
𝐭𝐢𝐧𝐲𝐩𝐥𝐨𝐭 v0.7.0 now available on CRAN 🎉 This is big release, with loads of new features. Same tiny footprint, though ;-) Short highlight thread below, borrowing examples from our gallery: grantmcdermott.com/tinyplot/vig...
https://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/bubble-quakes.Rhttps://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/simpsons-paradox.Rhttps://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/barplot-meat.Rhttps://github.com/grantmcdermott/tinyplot/blob/main/vignettes/gallery_figs/spineplot-titanic.R
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D. Griffin Jones @dgriffinjones.tech.lgbt.ap.brid.gy · 30/06/2026
Welp… it’s my turn to #getfedihired: • Experienced writer, primarily in technology news/reviews/how-tos • Professional audio and video editing for podcasts, YouTube, shorts • 20+ years in graphic design • 8 years as a marketing director • Computer Science degree • Based in Ohio, prefer remote […]
tech.lgbt
Original post on tech.lgbt
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Reposted by Thomas Sandmann
Simon Willison @simon.fedi.simonwillison.net.ap.brid.gy · 22/06/2026
I just released the first release candidate for sqlite-utils v4, adding a migrations system (previously released independently as sqlite-migrate) and support for nested transactions: simonwillison.net/2026/Jun/21/sqlit…
simonwillison.net
sqlite-utils 4.0rc1 adds migrations and nested transactions
sqlite-utils is my combined Python library and CLI tool for working with SQLite databases. It provides an extensive set of higher-level operations on top of Python’s default sqlite3 package, including …
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hrbrmstr 🇺🇦 🇬🇱 🇨🇦🇧🇪 @hrbrmstr.mastodon.social.ap.brid.gy · 19/06/2026
Drop #780 (2026-06-19): SSHHHH 🤫📝 Today's Drop discusses various useful SSH features and tips to improve automation and efficiency when using SSH. Key highlights include using BatchMode to avoid hanging connections, running local shell functions on remote hosts, maintaining sessions with […]
mastodon.social
Original post on mastodon.social
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Tom Stafford @tomstafford.mastodon.online.ap.brid.gy · 15/06/2026
TODAY: Listening to Richard McElreath "A Guerrilla Approach to Scientific Workflow" peercommunityin.org/pci-webinar-ser… Here's a dispiriting chart he shared from Serra-Garcia & Gneezy 2021 doi.org/10.1126/sciadv.abd1705 "Nonreplicable […] [Original post on mastodon.online]
Fig. 3 Yearly citation count by replicability.
The average yearly citation count per year for studies that were not replicated (according to P value of the replication) in each replication study [(A) for Nature/Science, (B) for Economics, and (C) for Psychology papers in replication markets] and for those that were replicated. The light gray area shows the year(s) in which the original studies were published, and the dark line shows the year in which the replication study was published.

Non-replicated papers increasingly cited above replicated
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Stephen Turner @stephenturner.us · 11/06/2026
Ten simple rules for teaching data science: journals.plos.org/ploscompbiol... 🧪 With a checklist in the SI
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hrbrmstr 🇺🇦 🇬🇱 🇨🇦🇧🇪 @hrbrmstr.mastodon.social.ap.brid.gy · 10/06/2026
With macOS 27 Apple also updated their `container` utility with a new `machine` command (that works on macOS 26 as well). It creates and manages lightweight Linux VMs (alpine/ubuntu/debian/perhaps more). I fired off a new blog post explaining it a bit, noting some "gotchas", and showcasing two […]
mastodon.social
Original post on mastodon.social
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@RonSupportsYou @ronsupportsyou.mastodon.social.ap.brid.gy · 06/06/2026
Sen. Raphael Warnock: "We’ve only been a democracy in a real sense since 1965. What we are witnessing in real time is an assault on those basic voting rights. I think that the Supreme Court has committed violence against the ways in which ordinary people can have a voice in our system" […]
mastodon.social
Original post on mastodon.social
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Lisa Melton @lisamelton.mastodon.social.ap.brid.gy · 06/06/2026
Would you like to play a demo of my new game? Sure you would! store.steampowered.com/app/4377480/… It's called "Burn-9," a turn-based tactical visual novel. You're the operator directing a super soldier fighting for her life in a secret Antarctic military base. The demo is short […]
mastodon.social
Original post on mastodon.social
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David Penfold :verified: @davep.infosec.exchange.ap.brid.gy · 06/06/2026
John Finnemore on the French horn/cor anglais: "I was idly wondering why the cor anglais has a French name meaning ‘English horn’, and the French horn has an English name meaning… well, ‘French horn’. I looked it up, even though I knew there would just be some reasonable but rather dull […]
infosec.exchange
Original post on infosec.exchange
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Tim Bray 🇨🇦 @timbray.cosocial.ca.ap.brid.gy · 05/06/2026
RE: mastodon.social/@gvwilson/116698825… The slides are excellent, I recommend reading them.
mastodon.social
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rOpenSci @handle.invalid · 29/05/2026
Meet Ezekiel Adebayo Ogundepo 🇳🇬 #MaintainerMonth Ezekiel is a data scientist with 10+ years of experience in interpreting and analyzing data in a fast-paced environment. As a rOpenSci Champion, Ezekiel worked on bulkreadr, an #RStats package to simplify and […] [Original post on hachyderm.io]
Ezekiel picture, Nigeria flag, social media accounts and personal website.
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rOpenSci @handle.invalid · 25/05/2026
👋 Meet Will Landau! 🇺🇸 Statistician and software developer. He maintains {targets} and several related packages to the targets ecosystem. Target is a pipeline toolkit that makes data analysis in R faster and fully reproducible by tracking dependencies and […] [Original post on hachyderm.io]
Will profile picture, github user and social media links
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Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 22/05/2026
I keep trying to use #rstats functions like table() and which() when I'm writing #python but those don't exist... until now jcarroll.com.au/2026/05/22/function… The rfuns package is live on pypi (my very first python package) and includes python-native functions with […]
fosstodon.org
Original post on fosstodon.org
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Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 21/05/2026
Linting prose around code with vale: jcarroll.xyz/2026/05/21/linting-pro…
jcarroll.xyz
Linting prose around code with vale
You may be familiar with the idea of linting for code, e.g. via {lintr} in R which “checks for adherence to a given style, identifying syntax errors and possible semantic issues.” It’s super helpful both for ensuring that your code meets your standards, but also when working in a team; no more arguing over nits in PRs about code style — it can be checked against your style guide rules automatically and enforced with tools like {styler}.
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rOpenSci @handle.invalid · 21/05/2026
👋 Today's highlight is Jeroen Ooms! 🇳🇱 Staff Research Engineer at rOpenSci, tidyverse team member, and project lead for R-universe. He also maintains {magick}, {pdftools}, and {gert} for rOpenSci. Find Jeroen at: 🐘 @jeroenooms 💻 github.com/jeroen 🌐 […] [Original post on hachyderm.io]
Jeroen picture, package list, personal website, GitHub user and mastodon account
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Clemens Schmid @clemensschmid.archaeo.social.ap.brid.gy · 19/05/2026
Positioning text labels in scatter plots is not always easy with #ggplot2, even with clever extensions like ggrepel. A new release of my #rstats package ggpointgrid aims to add another string to our bow here. To show what I mean I wrote a little blog post with […] [Original post on archaeo.social]
Example plot 2: Labels around a polygonExample plot 1: Labels on a lineExample plot 3: Labels on a grid around a point cloud
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rOpenSci @handle.invalid · 19/05/2026
👋 Meet Jonathan Keane! Engineer at Posit, formerly at Ursa Computing, Voltron Data, and Socure. Jon maintains {dittodb} for rOpenSci: a package that makes testing database code easy by recording and replaying real database interactions, so tests run without […] [Original post on hachyderm.io]
Jon picture, bio, social media handles, Github user and package name.
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rOpenSci @handle.invalid · 18/05/2026
👋 Meet Mark Padgham! 🇩🇪 rOpenSci Software Review Lead and maintainer of {pkgcheck}. This package checks whether a package is ready for submission to our software peer review and is very useful for R package developers to check their own packages against our […] [Original post on hachyderm.io]
Mark headshot, German flag, personal website, github user and social media handle.
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rOpenSci @handle.invalid · 15/05/2026
👋 Meet Karl Broman! 🇺🇸 Professor of Biostatistics & Medical Informatics at UW–Madison and applied statistician working on statistical genomics. He maintains {chromer} and {aRxiv}. Both packages provide programmatic access to APIs: Chromosome Counts Database and […] [Original post on hachyderm.io]
Karl headshot, package list, pesonal website, github user and social media.
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Stephen Turner @stephenturner.us · 15/05/2026
anndataR improves interoperability between #Rstats and Python in single-cell transcriptomics academic.oup.com/bioinformati...
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Diomidis Spinellis @coolsweng.mastodon.acm.org.ap.brid.gy · 07/05/2026
Today we launch a new run of the popular and award-winning free massive online course (MOOC) on the use of Unix Tools for data, software and production engineering. More than 7,500 learners enrolled on edX. Now, a further reason to follow the course is to […] [Original post on mastodon.acm.org]
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Thomas Sandmann @thomas-sandmann.genomic.social.ap.brid.gy · 08/05/2026
@brianvastag We have used TrustedHouseSitter a few times, it worked well for us. You get to interview the sitters, usually on a video call, that takes a bit of getting used to (assuming you are looking for a sitter, not a sit). Would do it again!
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Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 04/05/2026
I've been looking into dbt for data engineering and wanted to flesh out what the similarities and differences were to just using {targets} - I learned lots about both of them! I wrote up my findings in this post […]
fosstodon.org
Original post on fosstodon.org
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Stephen Turner @stephenturner.us · 03/05/2026
Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪
doi.org
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
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Christopher Neugebauer @fedi.chrisjrn.fyi · 01/05/2026
This blog post from @pythonbynight captures so much of what we try to do at #NBPy: a tech conference about people, a schedule that gives presenters the time they need to tell their story, speakers who are just another part of the audience. I love that what we're trying to do shines through with […]
social.coop
Original post on social.coop
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Steve Bellovin @stevebellovin.infosec.exchange.ap.brid.gy · 30/04/2026
New book, released under a Creative Commons BY-NC-ND license: "Don't Get Hacked! Protecting Yourself at Home": www.cs.columbia.edu/~smb/homesec/in… Retoot for reach!
cs.columbia.edu
Don't Get Hacked!
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Paco Hope @paco.infosec.exchange.ap.brid.gy · 24/04/2026
"It's called _vibe plumbing_. I'm not even a plumber. Soon, all swimming pools will be done this way! Get onboard or get left behind." (a real life version of the 'vibe construction' comic from mandatoryrollercoaster.com). Photo taken from plumbers fails)
Photo of a very complicated swimming pool set up. It has multiple pumps and multiple filters and a rats nest of PVC tubing going all kinds of wacky different directions. Unlike my caption, which mocks AI, the photo appears to be dated 2017, so it seems like it might be real.
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Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 24/04/2026
I've been keeping an eye on this since I first heard about it, and it looks like it now works! duckdb has a dplyr extension which can be installed - use dplyr code to slice and dice data within a duckdb session […] [Original post on fosstodon.org]
dplyr code running within a duckdb session
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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 23/04/2026
Pleased to share with you our latest article "Ten common mistakes that could ruin your enrichment analysis", featuring Anusuiya Bora, Matthew McKenzie. This article condenses what we've learned about best practices in pathway enrichment analysis over the past 15 years. We hope you find it […]
genomic.social
Original post on genomic.social
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Thomas Sandmann @thomas-sandmann.genomic.social.ap.brid.gy · 18/04/2026
@jonocarroll I had a chance to work with @jonocarroll - highly recommended!
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Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 18/04/2026
A bit of a long shot, but in the spirit of #fedihire I'm on the lookout for opportunities to contribute to R tooling. If your org could use some help developing or productionising an R package or some prototype R code, managing data access via databases or APIs, or translating between languages […]
fosstodon.org
Original post on fosstodon.org
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Jonathan Carroll @jonocarroll.fosstodon.org.ap.brid.gy · 14/04/2026
R/Pharma 2026 call for speakers is open until (approx) 02 May and we're once again running an APAC track for those not in North America/Europe timezones. Some of last year's sessions are available on YouTube www.youtube.com/rinpharma We're interested […] [Original post on fosstodon.org]
R/Pharma logo image
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Miguel de Icaza ᯅ🍉 @migueldeicaza.mastodon.social.ap.brid.gy · 06/04/2026
This is an amazing thread, holy shit.
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Bastian Greshake Tzovaras @gedankenstuecke.scholar.social.ap.brid.gy · 04/04/2026
«Every hour you spend confused is an hour you spend building the infrastructure inside your own head that will eventually let you do original work. There is no shortcut through that process that doesn't leave you diminished on the other side.» The machines are fine. I'm worried about us […]
scholar.social
Original post on scholar.social
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Grant McDermott @gmcd.bsky.social · 01/04/2026
1. `tinyplot` v0.6.1 is out on CRAN. This release contains mostly bug fixes and internal optimizations. grantmcdermott.com/tinyplot/NEW... Who knew that base #rstats plotting could be this easy and feature-rich? P.S. Check out @zeileis.org's nice slides here: www.zeileis.org/papers/Psych...
tinyplot boxplot with jittered points
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