Michael Love

@mikelove.bsky.social

7043 Followers 1829 Following

Genetics, bioinformatics, comp bio, statistics, data science, open source, open science!

Screen shot showing the beginning of the appendix for the workflow, with updated details on quantification.
Screen shot of the quick start instructions. Prepare exons, preprocess, then find splicing events. See the github page for the rest of the quick start code and installation instructions.
Code from the tximeta vignette showing how to build a DGEList object.
What has been the most instructive moment in your scientific career? Being as open as possible about your results and sharing data. In many projects, I’ve received crucial feedback because we shared our results openly and publicly, often before we had published a paper or even a preprint. In my experience, you shouldn’t fear that someone will steal your results. A much bigger risk is that there’s an important error in your analysis or experiment that you’ve missed, but which could be spotted quickly in a short conversation.
"Hertzsprung–Russell diagram. A plot of luminosity (absolute magnitude) against the colour of the stars ranging from the high-temperature blue-white stars on the left side of the diagram to the low temperature red stars on the right side."
Snippet from slide showing power curves
Meeting agenda Sep 10, 2025 Attendees: Links: Agenda (feel free to add your items): • Blog almost ready for R blogger linkage thanks to @Izabela Mamede, @Mengyuan Shen and @Maria Doyle • New posts from many including @Juan Henao and myself • Ideas for other posts? • There is tidybulk v2 ready to be submitted. Some feedback would be nice there. • Stefano's new speedy code in tidySE • https://github.com/tidyomics/ genomics-todos/issues/19#is suecomment-3239791713 • https://github.com/tidyomics/t idySummarizedExperiment/i ssues/106 • Report back from tidyomics workshop at useR! (Justin and Mike) • Other projects in the works? • Ideas for engaging new users? New developers?
A ChatGPT question: What DESeq2 design and contrast should I use if I have three conditions (control, drug A, drug B), two time points (pre and post), and a number of donors, with donors nested within the conditions. E.g. a donor is in only one of the condition groups, and each donor has a pre and post sample. I want to compare the effects across conditions, but control for donor effects. Answer: Got it — you've got a repeated-measures structure (pre vs. post within each donor), but donors are nested inside condition groups (no donor appears in multiple conditions). Here's how you can set up the DESeq2 design: ...
Figure from referenced preprint, colocalization increasing with larger sample size.
Table from the referenced preprint. Percentage signals detected across a range of sample size.
Table from the referenced preprint, power by signal strength and sample size.
Beatriz Campillo in front of a slideshow
Justin Landis in front of podium with slides: What is Bloconductor? Bioconductor is an open-source project that provides tools for the analysis and comprehension of high-throughput genomic data...
"When you vibe code, you are incurring tech debt as fast as the LLM can spit it out. Which is why vibe coding is perfect for prototypes and throwaway projects: It' s only legacy code if you have to maintain it! !...] The worst possible situation is to have a non-programmer vibe code a large project that they intend to maintain. This would be the equivalent of giving a credit card to a child without first explaining the concept of debt. [...]"
Recs from the linked paper
Photo of Mike, Yuriko and Will
Alex at the podium with Mike standing in the background
Speaker at podium holding book in one hand and loose pages in another
Scholarship Tiers: • Tier 1 (registration + travel support up to $700) is limited and highly competitive. Only select this if you cannot attend without travel funding. A brief justification is required. • Tier 2 (registration only) is for applicants who can cover their own travel. You must confirm that travel funding is secured. • Tier 3 will cover the VIRTUAL conference registration only. What Registration Includes (Tiers 1 & 2) • Full access to sessions, workshops, and networking events • Daily meals (breakfast, lunch, dinner) • Welcome reception and banquet • On-campus housing • Free on-site parking
Table of treatment (rows) and trait (columns) for colocalization of eQTL with GWAS
Sayan Mukherjee
PRELIMINARY STATEMENT This case involves an unprecedented threat from the Trump administration to withhold nearly nine billion dollars in federal funding to one of our nation's leading universities unless it accedes to changes that fundamentally compromise the university's independence and the free speech rights of its faculty and students. On March 31, 2025, Defendants' announced an investigation into federal grants that support critical research projects at Harvard University. On April 3, as a result of that investigation, Defendants made clear that funding would be terminated if Harvard did not "immediate[ly]" implement a litany of sweeping but vaguely-worded demands for changes to university operations, governance, hiring, admissions, curriculum, and student discipline. There is no doubt that, absent Harvard's capitulation to these demands, the cancellation of federal funding is imminent: Defendants have already cancelled or frozen hundreds of millions of dollars in funding for other universities that have been similarly targeted, with further cuts still threatened.
Colorful flowers
Image of Noor defending
text from linfo.org "Pipes rank alongside the hierarchical file system and regular expressions as one of the most powerful yet elegant features of Unix-like operating systems. ..."
Screenshot of workflow from Jayaram's BioC2024 workshop
Wizard sitting on a rock holding a stick into a creek "Hey did you hear about the drama betwe-" "No."
Joe Ibrahim, Naim Rashid, me, Didong Li, and Huitong Shi at Naim's tenure party
Milliseconds of time elapsed for joins on various sized datasets. Roughly, 1e3 = 7 ms, 1e4 = 8 ms, 1e5 = 20 ms, 1e6 = 200 ms.
Plyranges apparent time elapsed always >1s for <10k ranges
Banner for STATGEN 2024: a conference on statistics in genomics and genetics
a screenshot of the announcement text (can be found by following link in the post)
Naim Rashid standing at a lecturn at UNC Chapel Hill
Heart shape emerging from a planter, out of clover, in front of a store
Picture of buildings and church spires in Luebeck, Germany
Lucian Lucian emails a call for papers
article about a town in France that banned scrolling smartphones in public
Probabilistic model of fragments for ambiguous reads
Course overview for GENE 220
Picture of Bernie “I’m once again…” meme
Tximeta Bioconductor package importing samples
Musical benches that swing around on the ground
Headline: Hertz ditches Tesla
Notice from GRC
Two cool guys one is holding a jade plant
13 foot great white shark being tagged
Isa and Jon discuss the bubonic plague
Picture of Libba Cotten
new Bioconductor website
Ptah the El Daoud - Alice Coltrane - album cover
Example code for making a legend with some equations and values inside: 20 legend("bottomright", 21 legend=c(dat$symbol[i], 22 dat$trait[i], 23 bquote(hat(alpha) == .(alpha_hat))), 24 inset = .05, bty="n")
Highlight of Fig 6: CDG GWAS, PCLO gene expression and ENST00000423517 isoform expression QTLs.
Xihao, Will and Mike at UNC Chapel Hill
Trees in a valley, orange, yellow and green
Memes would help.
Dhuvi and Andy at the BCB/GMB retreat