Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Orchestrating Microbiome Analysis with Bioconductor
The expansion of microbiome research has led to the accumulation of interlinked datasets encompassing versatile taxonomic and functional assays. The analysis of increasingly large and heterogeneous…
www.biorxiv.org
November 9, 2025 at 11:31 AM
Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
🎓 Upcoming Online Course: R/Bioconductor for Mass Spectrometry & Proteomics
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
R/Bioconductor for Mass Spectrometry and Proteomics
Dates 17-19 November 2025 To foster international participation, this course will be held online
www.physalia-courses.org
November 6, 2025 at 10:00 AM
🎓 Upcoming Online Course: R/Bioconductor for Mass Spectrometry & Proteomics
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
📅 November 17–19, 2025
Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.
👉 Register & learn more: www.physalia-courses.org/courses-work...
Lots of new + interesting stuff in Bioconductor 3.22 blog.stephenturner.us/p/bioconduct... #Rstats
Bioconductor 3.22 Released
59 new software packages, updates for genomics, single-cell transcriptomics, spatial omics, QC tooling, core I/O, GFF/CIGAR handling, much more.
blog.stephenturner.us
October 31, 2025 at 5:45 PM
Lots of new + interesting stuff in Bioconductor 3.22 blog.stephenturner.us/p/bioconduct... #Rstats
Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1
October 30, 2025 at 8:54 PM
Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
October 29, 2025 at 9:02 AM
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Save the date! Bioconductor 2026 will be held at Fred Hutch in Seattle, WA. #rstats August 10-12, includes a developer day!
bioc2026.bioconductor.org
Stay tuned for more details, including how to submit abstracts!
bioc2026.bioconductor.org
Stay tuned for more details, including how to submit abstracts!
Bioconductor
bioc2026.bioconductor.org
October 28, 2025 at 4:25 PM
Save the date! Bioconductor 2026 will be held at Fred Hutch in Seattle, WA. #rstats August 10-12, includes a developer day!
bioc2026.bioconductor.org
Stay tuned for more details, including how to submit abstracts!
bioc2026.bioconductor.org
Stay tuned for more details, including how to submit abstracts!
Thank you to all our amazing sponsors, organizers, speakers, and attendees for making #EuroBioC2025 in Barcelona such a success!
Read the full recap blog post here👉 blog.bioconductor.org/posts/2025-1...
And, see you next year at #EuroBioC2026! 🎉
#Bioconductor #Community #Conference
Read the full recap blog post here👉 blog.bioconductor.org/posts/2025-1...
And, see you next year at #EuroBioC2026! 🎉
#Bioconductor #Community #Conference
EuroBioC2025 conference recap – Bioconductor community blog
Highlights from the 2025 European Bioconductor Conference in Barcelona
blog.bioconductor.org
October 24, 2025 at 1:00 PM
Thank you to all our amazing sponsors, organizers, speakers, and attendees for making #EuroBioC2025 in Barcelona such a success!
Read the full recap blog post here👉 blog.bioconductor.org/posts/2025-1...
And, see you next year at #EuroBioC2026! 🎉
#Bioconductor #Community #Conference
Read the full recap blog post here👉 blog.bioconductor.org/posts/2025-1...
And, see you next year at #EuroBioC2026! 🎉
#Bioconductor #Community #Conference
Weekly recap: Bioconductor on GPUs, tidyomics, Quarto 1.8, Anthropic red-teaming on AIxBio, PGS in the clinic, Shock Doctrine in genome engineering, GenAI for data viz with #Rstats, Datapalooza, 4 compact rejections, more... blog.stephenturner.us/p/weekly-rec... 🧬🖥️🧪
October 17, 2025 at 12:41 PM
Weekly recap: Bioconductor on GPUs, tidyomics, Quarto 1.8, Anthropic red-teaming on AIxBio, PGS in the clinic, Shock Doctrine in genome engineering, GenAI for data viz with #Rstats, Datapalooza, 4 compact rejections, more... blog.stephenturner.us/p/weekly-rec... 🧬🖥️🧪
We previously developed DMRcaller, a Bioconductor package for the analysis of DNA methylation data from WGBS (academic.oup.com/nar/article/...). This is a highly versatile tool that allows great flexibility in detecting Differential DNA methylation in CpG and non-CpG context.
October 14, 2025 at 8:21 AM
We previously developed DMRcaller, a Bioconductor package for the analysis of DNA methylation data from WGBS (academic.oup.com/nar/article/...). This is a highly versatile tool that allows great flexibility in detecting Differential DNA methylation in CpG and non-CpG context.
GeDi: Simplifying Gene Set Distances for Enhanced Omics Interpretation in R/Bioconductor
doi.org/10.1101/2025...
doi.org/10.1101/2025...
GeDi: Simplifying Gene Set Distances for Enhanced Omics Interpretation in R/Bioconductor
Background: Functional enrichment analysis is a standard component in many omics data analysis workflows, supported by a variety of methods and algorithms. However, despite their utility and wide appl...
doi.org
October 13, 2025 at 8:26 PM
GeDi: Simplifying Gene Set Distances for Enhanced Omics Interpretation in R/Bioconductor
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford’s HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But the lesson was worth it
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
My Attempt To Reproduce Stanford HIVdb Sequence and Mutation Analysis From Scratch | Everyday Is A School Day
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford's HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But th...
www.kenkoonwong.com
October 11, 2025 at 3:51 AM
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford’s HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But the lesson was worth it
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
My first CRAN package! 🤓
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
New on CRAN: SimpleUpset (0.1.2). View at https://CRAN.R-project.org/package=SimpleUpset
SimpleUpset: Create Upset Plots
Create Upset plots using a combination of 'ggplot2' and 'patchwork'.
CRAN.R-project.org
October 7, 2025 at 1:01 AM
My first CRAN package! 🤓
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
🌟 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.
🌍 Applications now open for our first Bioconductor course in West Africa!
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
October 1, 2025 at 2:32 PM
🌍 Applications now open for our first Bioconductor course in West Africa!
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
Open seminar on open science! MBC had the great pleasure to host Alexandru Mahmoud from the Bioconductor Core Team. Automatic workshop creation with BuildABiocWorkshop will surely accelerate teaching of bioinformatics. Thanks, Alex!
@bioconductor.bsky.social @turkubioscience.bsky.social @utu.fi
@bioconductor.bsky.social @turkubioscience.bsky.social @utu.fi
October 1, 2025 at 1:00 PM
Open seminar on open science! MBC had the great pleasure to host Alexandru Mahmoud from the Bioconductor Core Team. Automatic workshop creation with BuildABiocWorkshop will surely accelerate teaching of bioinformatics. Thanks, Alex!
@bioconductor.bsky.social @turkubioscience.bsky.social @utu.fi
@bioconductor.bsky.social @turkubioscience.bsky.social @utu.fi
Learned RNA-seq workflow using C. diff data from a study 🧬. Processed raw reads thru fastp → kallisto → DESeq2 pipeline. Results matched the original paper’s findings, with clear differential expression between mucus and control conditions 📊.
#idsky #microsky #rstats #deseq2 #bioconductor
#idsky #microsky #rstats #deseq2 #bioconductor
Learning And Exploring The Workflow of RNA-Seq Analysis - A Note To Myself | Everyday Is A School Day
Learned RNA-seq workflow using C. difficile data from a published study 🧬. Processed raw reads through fastp → kallisto → DESeq2 pipeline. Results matched the original paper's findings, with clear dif...
www.kenkoonwong.com
September 27, 2025 at 9:00 PM
Learned RNA-seq workflow using C. diff data from a study 🧬. Processed raw reads thru fastp → kallisto → DESeq2 pipeline. Results matched the original paper’s findings, with clear differential expression between mucus and control conditions 📊.
#idsky #microsky #rstats #deseq2 #bioconductor
#idsky #microsky #rstats #deseq2 #bioconductor
#EuroBioC2025 is over and it has been a blast! Thanks to all participants that came to @prbb.org for contributing to make such an enjoyable event and special thanks to the support from our sponsors, the organizing institutions @upf.edu @isglobal.org and the European @bioconductor.bsky.social Society
September 19, 2025 at 5:32 PM
#EuroBioC2025 is over and it has been a blast! Thanks to all participants that came to @prbb.org for contributing to make such an enjoyable event and special thanks to the support from our sponsors, the organizing institutions @upf.edu @isglobal.org and the European @bioconductor.bsky.social Society
I am the 1st woman for #Switzerland🇨🇭 to develop the R package in #Bioconductor, aka software development during my doctorate. shorturl.at/e0PVw (GitHub link); shorturl.at/BDLPx (Bioconductor link) #1stwomanforswitzerland #missdrkomljenovic #switzerland 🇨🇭
GitHub - wirawara/BgeeDB: an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests, Komljenovic et al. f1000Research
an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests, Komljenovic et al. f1000Research - GitHub - wirawara/BgeeDB: an R package for ...
shorturl.at
September 18, 2025 at 3:31 PM
I am the 1st woman for #Switzerland🇨🇭 to develop the R package in #Bioconductor, aka software development during my doctorate. shorturl.at/e0PVw (GitHub link); shorturl.at/BDLPx (Bioconductor link) #1stwomanforswitzerland #missdrkomljenovic #switzerland 🇨🇭
EuroBioC2025 is in full swing here in Barcelona!
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
September 18, 2025 at 9:53 AM
EuroBioC2025 is in full swing here in Barcelona!
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Luca Marconato at the European Bioconductor Conference 2025 in Barcelona, on advancing spatial biology analysis across programming languages — R, Python, JS.
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
September 18, 2025 at 9:29 AM
Luca Marconato at the European Bioconductor Conference 2025 in Barcelona, on advancing spatial biology analysis across programming languages — R, Python, JS.
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
BarbieQ: Our new paper outlining our bioconductor package for the statistical analysis of barcode count data. Lineage tracing and clonal tracking. They made us add the Q
September 16, 2025 at 12:42 AM
BarbieQ: Our new paper outlining our bioconductor package for the statistical analysis of barcode count data. Lineage tracing and clonal tracking. They made us add the Q
Interoperability of Bioconductor packages within the ELIXIR Research Software Ecosystem using the EDAM ontology - CNRS - Centre national de la recherche scientifique cnrs.hal.science/hal-05250261v1
Interoperability of Bioconductor packages within the ELIXIR Research Software Ecosystem using the EDAM ontology
Bioconductor packages are currently annotated using the biocViews controlled vocabulary (Carey et al., 2024), structured as a graph with nearly 500 terms, of which 175 are meant for software annotatio...
cnrs.hal.science
September 16, 2025 at 5:19 AM
Interoperability of Bioconductor packages within the ELIXIR Research Software Ecosystem using the EDAM ontology - CNRS - Centre national de la recherche scientifique cnrs.hal.science/hal-05250261v1
From @cp-patterns.bsky.social | #Bioconductor: Planning a third decade of comprehensive support for genomic data science | #Bioinformatics #Genomics #OpenScience #OpenSource 🧬 🖥️ 🧪 🔓
⬇️
www.cell.com/patterns/ful...
⬇️
www.cell.com/patterns/ful...
Bioconductor: Planning a third decade of comprehensive support for genomic data science
This opinion piece discusses the Bioconductor project for open-source bioinformatics
and the engineering concepts underlying its effectiveness to date. Since the inception
of Bioconductor in 2002 with...
www.cell.com
September 11, 2025 at 12:58 PM
From @cp-patterns.bsky.social | #Bioconductor: Planning a third decade of comprehensive support for genomic data science | #Bioinformatics #Genomics #OpenScience #OpenSource 🧬 🖥️ 🧪 🔓
⬇️
www.cell.com/patterns/ful...
⬇️
www.cell.com/patterns/ful...
CSAMA one-week summer school biological data science, in Brixen/Bressanone, South Tyrol, 23-28 June. Register now for one of the last places. Topics include single cell omics, statistical foundations, R/Bioconductor tools, mass spec, interactive workflows
csama2024.bioconductor.eu
csama2024.bioconductor.eu
May 21, 2024 at 3:13 PM
CSAMA one-week summer school biological data science, in Brixen/Bressanone, South Tyrol, 23-28 June. Register now for one of the last places. Topics include single cell omics, statistical foundations, R/Bioconductor tools, mass spec, interactive workflows
csama2024.bioconductor.eu
csama2024.bioconductor.eu