David Rach
@davidrach.bsky.social
Immunology PhD student @UMBaltimore. Views are my own. Favorite rabbit holes include #flowcytometry #rstats #bioconductor, with dashes of #coffee #kayaking #birding #ultrunning #languages. RPCV Ghana 16->18, TCK Mexico 96->11 https://github.com/DavidRach/
Pinned
David Rach
@davidrach.bsky.social
· Aug 25
Frontiers | Cord blood innate-like T cell responses in neonates born to healthy women and women living with HIV
Innate-like T cells (ILT), including γδ T cells (Vδ2s), Natural Killer T cells (NKTs) and Mucosal-associated Invariant T cells (MAITs), integrate innate and ...
www.frontiersin.org
Our paper on cord blood innate-like T cell responses in HIV-exposed but Uninfected (HEU) infants is (finally) out! 🎉😅😄 Writing was slowed due to my constant diving into #flowcytometry, #rstats and #gdtcell rabbit-holes. See how these all converged below. 1/n
www.frontiersin.org/journals/imm...
www.frontiersin.org/journals/imm...
Reposted by David Rach
My talk from posit::conf earlier this fall on getting unstuck with #Python is now available to watch!
- Ten years ago, I attempted to learn Python and it went EXTRMELY badly 😩
- I am really happy that so much tooling in this area has improved SO much since then 😌
youtu.be/pMVYl9fx1EE
- Ten years ago, I attempted to learn Python and it went EXTRMELY badly 😩
- I am really happy that so much tooling in this area has improved SO much since then 😌
youtu.be/pMVYl9fx1EE
How I got unstuck with Python (Julia Silge, Posit) | posit::conf(2025)
YouTube video by Posit PBC
youtu.be
November 8, 2025 at 11:59 PM
My talk from posit::conf earlier this fall on getting unstuck with #Python is now available to watch!
- Ten years ago, I attempted to learn Python and it went EXTRMELY badly 😩
- I am really happy that so much tooling in this area has improved SO much since then 😌
youtu.be/pMVYl9fx1EE
- Ten years ago, I attempted to learn Python and it went EXTRMELY badly 😩
- I am really happy that so much tooling in this area has improved SO much since then 😌
youtu.be/pMVYl9fx1EE
Reposted by David Rach
Just restocked a lot of stickers including these guys!
(shop.emibirdee.com/products/be-...)
(shop.emibirdee.com/products/be-...)
November 9, 2025 at 10:32 PM
Just restocked a lot of stickers including these guys!
(shop.emibirdee.com/products/be-...)
(shop.emibirdee.com/products/be-...)
Reposted by David Rach
This is an amazing (and infuriating) story, complete with Github repos of their analysis!
November 8, 2025 at 7:08 PM
This is an amazing (and infuriating) story, complete with Github repos of their analysis!
Reposted by David Rach
This obit of Watson is *amazing*.
A Sharon Begley byline, almost 5 years after her death.
Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."
Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating.
🧪🧬🧫
Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."
Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating.
🧪🧬🧫
James Watson, dead at 97, was a scientific legend and a pariah among his peers
James Watson, the co-discoverer of the structure of DNA who died Thursday at 97, was a scientific legend and a pariah among his peers.
www.statnews.com
November 8, 2025 at 8:14 PM
This obit of Watson is *amazing*.
Happy to officially announce that we are hosting a free “Cytometry in R” weekly mini-course, aimed at coding beginners, both in-person here at the University of Maryland, Baltimore and virtually, starting up in December/January. For details: umgccfcss.github.io/CytometryInR/ #rstats #flowcytometry
November 5, 2025 at 9:36 PM
Happy to officially announce that we are hosting a free “Cytometry in R” weekly mini-course, aimed at coding beginners, both in-person here at the University of Maryland, Baltimore and virtually, starting up in December/January. For details: umgccfcss.github.io/CytometryInR/ #rstats #flowcytometry
Reposted by David Rach
Huge credit to @colibricytometry.bsky.social, who has spent years working on every aspect of the spectral flow cytometry pipeline. Follow the Colibri blog to get tips in real-time, pre-pre-print!
www.colibri-cytometry.com
www.colibri-cytometry.com
Cytometry Colibri | flow cytometry
Cytometry Colibri offers scientific consulting, data analysis, panel design, method development, tutoring and all things related to flow cytometry.
Expertise in high parameter flow cytometry, spectra...
www.colibri-cytometry.com
October 28, 2025 at 8:06 AM
Huge credit to @colibricytometry.bsky.social, who has spent years working on every aspect of the spectral flow cytometry pipeline. Follow the Colibri blog to get tips in real-time, pre-pre-print!
www.colibri-cytometry.com
www.colibri-cytometry.com
Reposted by David Rach
First, pos-neg gating. Ideal controls are your actual antibodies on the actual cells. However different antibodies bind different cells (see: CD4 vs XCR1 below), meaning they have different backgrounds to control. AutoSpectral matches the FSC-SSC of each pos to a suitable neg: with results!
October 28, 2025 at 8:06 AM
First, pos-neg gating. Ideal controls are your actual antibodies on the actual cells. However different antibodies bind different cells (see: CD4 vs XCR1 below), meaning they have different backgrounds to control. AutoSpectral matches the FSC-SSC of each pos to a suitable neg: with results!
Reposted by David Rach
💡 Came across this nice tool today:
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
Qualpal: Qualitative Color Palettes for Everyone
Larsson, J., (2025). Qualpal: Qualitative Color Palettes for Everyone. Journal of Open Source Software, 10(114), 8936, https://doi.org/10.21105/joss.08936
joss.theoj.org
October 17, 2025 at 9:12 AM
💡 Came across this nice tool today:
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
Reposted by David Rach
If you're one of the 0.5 people who actually use any of my #rstats packages: please, please, please send a PR my way with your beginner-friendly docs rather than make a new resource. I'll make you an official author and everything...
#RStats question:
Is there a package or site that provides alternative, more explanatory help files?
I swear a project like this exists, perhaps targeted to beginning R users, maybe centered around common data analysis functions, but I can't find it...
Is there a package or site that provides alternative, more explanatory help files?
I swear a project like this exists, perhaps targeted to beginning R users, maybe centered around common data analysis functions, but I can't find it...
October 18, 2025 at 2:22 PM
If you're one of the 0.5 people who actually use any of my #rstats packages: please, please, please send a PR my way with your beginner-friendly docs rather than make a new resource. I'll make you an official author and everything...
Reposted by David Rach
Still time to join our Flow Cytometry Core at the University of Aberdeen as a lead scientist
We're looking for a Lead Scientist to join Flow Cytometry Centre in Aberdeen! Fantastic opportunity to deliver services, work with varied research groups, promote cytometry and further develop the facility. Aberdeen is a great place to live/work- APPLY NOW www.abdnjobs.co.uk/vacancy/cyto...
Cytometry Facility Lead Scientist (IMS313A) | University of Aberdeen
A Lead Cytometry expert post is available for a highly motivated flow cytometrist to deliver cytometry services, promote and develop the Iain Fraser Cytometry Centre (IFCC). This post is for a highly...
www.abdnjobs.co.uk
October 15, 2025 at 3:26 PM
Still time to join our Flow Cytometry Core at the University of Aberdeen as a lead scientist
Reposted by David Rach
Teaching scientists about statistics is not even that difficult. But it slows down how many papers get published, so we can't do it. I mean, why would we put any brakes on LLM produced papers by insisting scientists and reviewers understand the output!? Madness.
As coding gets more plug and play, it becomes IMPERATIVE for us as educators to teach fundamentals about what the statistical tests are comparing and assumptions.
Students might not need to understand how to code things up, but they should understand what the snippets are doing and why
Students might not need to understand how to code things up, but they should understand what the snippets are doing and why
Y'all. I just got ChatGPT to do everything in R for this manuscript. I mean EVERYTHING. And it's all legit and reproducible. I'm shook.
How are we mentoring our trainees in statistics now? Who needs to learn coding in R line by line, and who doesn't?
scienceforeveryone.science/statistics-i...
How are we mentoring our trainees in statistics now? Who needs to learn coding in R line by line, and who doesn't?
scienceforeveryone.science/statistics-i...
October 11, 2025 at 11:21 AM
Teaching scientists about statistics is not even that difficult. But it slows down how many papers get published, so we can't do it. I mean, why would we put any brakes on LLM produced papers by insisting scientists and reviewers understand the output!? Madness.
Reposted by David Rach
Very proud of our team at the @i3h-upenn.bsky.social, for publishing an article that I believe contributes to a deeper and more robust analysis of cytometry data, enabling the scale-up of human immune profiling. #immunology #cytometry onlinelibrary.wiley.com/doi/10.1002/...
Cleanet: Robust Doublet Detection in Cytometry Data Based on Protein Expression Patterns
Flow and mass cytometry experiments are essential for profiling immune cells at single-cell resolution. Better understanding of human immunology increasingly involves analyzing studies at the scale o...
onlinelibrary.wiley.com
October 9, 2025 at 3:35 PM
Very proud of our team at the @i3h-upenn.bsky.social, for publishing an article that I believe contributes to a deeper and more robust analysis of cytometry data, enabling the scale-up of human immune profiling. #immunology #cytometry onlinelibrary.wiley.com/doi/10.1002/...
Reposted by David Rach
Citizen science gamers enable automated flow cytometry gating through machine learning https://www.biorxiv.org/content/10.1101/2025.10.07.679685v1
October 8, 2025 at 7:47 AM
Citizen science gamers enable automated flow cytometry gating through machine learning https://www.biorxiv.org/content/10.1101/2025.10.07.679685v1
Reposted by David Rach
🌟 Save the Date! BioC2026 is Coming! 🌟 Mark your calendars for August 10-12, 2026, at Fred Hutch Cancer Center, Seattle, WA, USA.
October 2, 2025 at 1:01 PM
🌟 Save the Date! BioC2026 is Coming! 🌟 Mark your calendars for August 10-12, 2026, at Fred Hutch Cancer Center, Seattle, WA, USA.
Reposted by David Rach
CytoScan: Automated detection of technical anomalies for cytometry quality control https://www.biorxiv.org/content/10.1101/2025.09.24.678276v1
September 26, 2025 at 9:47 PM
CytoScan: Automated detection of technical anomalies for cytometry quality control https://www.biorxiv.org/content/10.1101/2025.09.24.678276v1
I am intrigued, but now need to track down the specific soap 😂
For our #flowcytometry peeps, would you like to have a single fix/perm protocol that is optimised for everything? One that preserves fluorophores while allowing simultaneous TF and cytokine staining? How about 100-fold cheaper?
You got it:
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
You got it:
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
currentprotocols.onlinelibrary.wiley.com
September 19, 2025 at 4:55 PM
I am intrigued, but now need to track down the specific soap 😂
"And that’s the other problem — the bigger one: how much people want this causality. They want to believe that we have the data and methods to show that a disease that wipes out bats leads to an 8% increase in infant mortality."
The Desperation of Causal Inference in Ecology
statmodeling.stat.columbia.edu/2025/09/15/t...
statmodeling.stat.columbia.edu/2025/09/15/t...
The Desperation of Causal Inference in Ecology | Statistical Modeling, Causal Inference, and Social Science
statmodeling.stat.columbia.edu
September 16, 2025 at 10:12 AM
"And that’s the other problem — the bigger one: how much people want this causality. They want to believe that we have the data and methods to show that a disease that wipes out bats leads to an 8% increase in infant mortality."
Reposted by David Rach
Reposted by David Rach
If anyone here on BlueSky directs or works in a shared resource/core facility and lives in the northeast of the US (or southeast of Canada!) please consider coming to NERLSCD 2025 in New Haven from October 8-10. We have great keynotes and tracks for genomics, flow cytometry, imaging, admin and more!
NERLSCD | A regional chapter of the Association of Biomolecular Resource Facilities
Exploring New Technologies to Drive Advances in Basic, Clinical and Translational Research.
nerlscd.abrf.org
September 10, 2025 at 6:46 PM
If anyone here on BlueSky directs or works in a shared resource/core facility and lives in the northeast of the US (or southeast of Canada!) please consider coming to NERLSCD 2025 in New Haven from October 8-10. We have great keynotes and tracks for genomics, flow cytometry, imaging, admin and more!
Reposted by David Rach
{grateful} 0.3.0 is now on CRAN. Hope it makes citing #rstats packages even easier!
pakillo.github.io/grateful/
New features 👇
pakillo.github.io/grateful/
New features 👇
September 9, 2025 at 6:16 PM
{grateful} 0.3.0 is now on CRAN. Hope it makes citing #rstats packages even easier!
pakillo.github.io/grateful/
New features 👇
pakillo.github.io/grateful/
New features 👇
Reposted by David Rach
Our paper on cord blood innate-like T cell responses in HIV-exposed but Uninfected (HEU) infants is (finally) out! 🎉😅😄 Writing was slowed due to my constant diving into #flowcytometry, #rstats and #gdtcell rabbit-holes. See how these all converged below. 1/n
www.frontiersin.org/journals/imm...
www.frontiersin.org/journals/imm...
Frontiers | Cord blood innate-like T cell responses in neonates born to healthy women and women living with HIV
Innate-like T cells (ILT), including γδ T cells (Vδ2s), Natural Killer T cells (NKTs) and Mucosal-associated Invariant T cells (MAITs), integrate innate and ...
www.frontiersin.org
August 25, 2025 at 4:44 AM
Our paper on cord blood innate-like T cell responses in HIV-exposed but Uninfected (HEU) infants is (finally) out! 🎉😅😄 Writing was slowed due to my constant diving into #flowcytometry, #rstats and #gdtcell rabbit-holes. See how these all converged below. 1/n
www.frontiersin.org/journals/imm...
www.frontiersin.org/journals/imm...