This effort started back in the early Visium days with our colleagues at the @lieberinstitute.bsky.social including @martinowk.bsky.social @kr-maynard.bsky.social @lcolladotor.bsky.social and others. Wonderful to have a complete release version out now. Thanks to everyone who contributed! π§¬π§ π
22.11.2025 15:22 β π 6 π 1 π¬ 0 π 0
This was a huge effort by many contributors, in particular @helucro.bsky.social @estellayixingdong.bsky.social @rgottardo.bsky.social @markrobinsonca.bsky.social @stephaniehicks.bsky.social , and the @bioconductor.bsky.social core team and community. Thank you everyone! π
22.11.2025 12:38 β π 5 π 1 π¬ 1 π 0
This contains extensive code examples, workflows, datasets, and discussion on data analysis workflows for spatial transcriptomics data using Bioconductor in R. Please check it out - feedback and suggestions welcome! bioconductor.org/books/OSTA/
22.11.2025 12:38 β π 1 π 1 π¬ 1 π 0
We are excited to share our online book and preprint on βOrchestrating Spatial Transcriptomics Analysis with Bioconductorβ!
22.11.2025 12:38 β π 18 π 12 π¬ 1 π 0
I am very excited to share this book! It has been so much to collaborate on the project. We hope you find it useful!
21.11.2025 22:11 β π 22 π 7 π¬ 0 π 0
Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1
21.11.2025 14:46 β π 13 π 10 π¬ 0 π 1
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
21.11.2025 17:39 β π 21 π 8 π¬ 0 π 0
Whether you're new to bioinformatics or a seasoned pro, OSTA covers everything that you need to know about spatial transcriptomics data analysis spanning both sequencing and imaging-based technologies within the Bioconductor framework π¨βπ»π§¬
Congrats to all the authors on this huge effort!
21.11.2025 19:44 β π 5 π 2 π¬ 0 π 0
Honored to have gotten to be a part of this! I vividly remember the very early days of spatial transcriptomics when we were all scratching our heads over what to do with all this new data! It's come a long way - congrats @helucro.bsky.social @lmweber.bsky.social and everyone who contributed to this!
21.11.2025 18:44 β π 14 π 3 π¬ 0 π 0
Many people hours, calls and messages later: OSTA is now βin (pre)printβ, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
Itβs been a joy working with you @estellayixingdong.bsky.social!
21.11.2025 17:31 β π 40 π 24 π¬ 1 π 4
so excited to share that our preprint characterizing the dorsal anterior cingulate cortex in post-mortem human brain from @lieberinstitute.bsky.social is out! we integrated matched SRT and snRNA-seq data to investigate agranularity and von Economo neurons
24.07.2025 01:53 β π 13 π 3 π¬ 1 π 3
Winter in Western Australia βοΈ
29.06.2025 12:38 β π 4 π 0 π¬ 0 π 0
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
Update: We greatly revised our paper and renamed it βHarnessing the Potential of Spatial Statistics for Spatial Omics Data with pastaβ.
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
27.06.2025 13:28 β π 12 π 7 π¬ 1 π 0
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
25.06.2025 14:29 β π 220 π 82 π¬ 5 π 10
Very excited to see this important work out led by the talented @mictott.bsky.social @boyiguo.bsky.social @jhubiostat.bsky.social! π§ͺπ§¬π₯οΈ
06.06.2025 17:34 β π 22 π 5 π¬ 1 π 0
my work with @stephaniehicks.bsky.social and @boyiguo.bsky.social has been published in Biostatistics! tldr: the mean-variance bias exists in SRT data & impacts SVG detection. we propose #spoon, available on @bioconductor.bsky.social, to address this! pmc.ncbi.nlm.nih.gov/articles/PMC... π€©
17.06.2025 00:17 β π 7 π 3 π¬ 2 π 0
Congratulations!
24.06.2025 01:11 β π 1 π 0 π¬ 1 π 0
Congratulations!! π
23.06.2025 02:56 β π 1 π 0 π¬ 0 π 0
Feels like a social media tipping point might have happened π¦π΅
13.11.2024 21:36 β π 8 π 0 π¬ 1 π 0
This morning I'm teaching an intro to single cell data science!
Feeling very appreciative to all the amazing developers in the #Bioconductor and open science #rstats communities! #Genomics π₯οΈ π§¬ #stats π©βπ¬
π stephaniehicks.com/singlecellde...
19.09.2023 11:12 β π 43 π 9 π¬ 2 π 1
One last visit to Washington DC before I leave for Boston πΊπΈ
04.09.2023 23:03 β π 2 π 0 π¬ 0 π 0
Hello world ππ€οΈ
01.09.2023 19:09 β π 11 π 0 π¬ 2 π 0
Account of the Saez-Rodriguez lab at EMBL-EBI and Heidelberg University. We integrate #omics data with mechanistic molecular knowledge into #opensource #ML methods
Website: https://saezlab.org/
GitHub: https://github.com/saezlab/
Citizen, Dad, Husband, Scientist, program officer at NSF, former biology professor and sports βexpertβ. Views are mine and do not represent my employer. Returning to social media on my personal time .
Postdoc from School of Mathematics and Statistics, University of Sydney - affiliated with Sydney Precision Data Science Center and Charles Perkins Center.
Bioinformatician | Computational method development | Spatial transcriptomics | Microbial metagenomes
Twitter/X @haoyin20
Vascular biologist
physicist, bioinformatics / biostats researcher at University of Heidelberg
Senior Research Associate in Bioinformatics & Computational Biology in the Oshlack Lab @petermaccc.bsky.social Australia. Mum. Sci-fi nerd. Cat person. Really loves cheese. And dancing.
Data Science, Computational Biology, Biotechnology, Neuropsychiatry
Changing the lives of people with schizophrenia and related mental illnesses. Learn more about our research at www.libd.org.
PhD student in Statistical Bioinformatics at the University of Zurich and the Swiss Institue of Bioinformatics
R advocate #rstats | PhD @CHUVLausanne @unil | Immunology, Immunotherapy, Single-Cell RNAseq, Spatial Transcriptomics, Statistics and Machine Learning. π·βΈοΈποΈ
Investigator Lieber Institute for Brain Development
Network (Graph) Scientist. Computational and Spatial Biology. Statistical Learning for Bioinformatics.
Freelancing: Biostats / Genomics / CRISPR
github.com/Jfortin1
Assist. Prof | Leiden University | Mucosal Immunology | Human Disease | Single-Cell | Organoids | former postdoc Mark Davis & Calvin Kuo Lab at Stanfordπ vanunenlab.org π
Postdoc at Lieber Institute for Brain Development. Brain molecular regulΒ° and gene expressΒ° in health, mood disorders, and neurodegen (and sex diffs therein)
Associate Professor and Research Dean at UVA School of Data Science, #Rstats enthusiast, dad, runner, guitar noise-maker. Views my own.
Web: https://datascience.virginia.edu/people/stephen-turner
Newsletter: https://blog.stephenturner.us
Bioconductor: Free, open-source software for rigorous, reproducible biological data analysis with R. Join our diverse community of developers and data scientists.
https://bioconductor.org/
Biomedical Data Science Center Director @CHUV. Professor at @UNIL and @EPFL. AI, ML, and statistical learning for high-dimensional (single-cell/spatial) data in clinical and translational medicine. Interdisciplinary scientist passionate about data.
Genomics initiative lead at @GoogleDeepMind.
Models from our team: Enformer, AlphaMissense, and AlphaGenome.
Postdoctoral neuroscientist at JHU working at the intersection of neural circuits, bioinformatics, and psychiatric disorders.
https://mictott.github.io
