Nico Kaiser
@n-kaiser.bsky.social
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PhD student in the field of computational microscopy and spatial omics.
reposted by
Nico Kaiser
Malte Kuehl
3 months ago
Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself? Or would you like to find a way to use biomedical tools using natural language? Then check out
biocontext.ai
, now out on bioRxiv:
www.biorxiv.org/content/10.1...
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reposted by
Nico Kaiser
bioRxiv SysBio
4 months ago
Community-based biomedical context to unlock agentic systems
https://www.biorxiv.org/content/10.1101/2025.07.21.665729v1
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reposted by
Nico Kaiser
Malte Kuehl
4 months ago
🚨Scaling multiplexed imaging 📈 We are excited to share Pathology-oriented multiPlexing (PathoPlex). Now out in
@nature.com
:
www.nature.com/articles/s41...
🧵Walk-through thread below ⬇️
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reposted by
Nico Kaiser
Malte Kuehl
11 months ago
Happy to share that pytximport has now been included in the December issue of Bioinformatics and can be read online without downloading the PDF:
doi.org/10.1093/bioi...
add a skeleton here at some point
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reposted by
Nico Kaiser
Lior Pachter
12 months ago
You can now run tximport in Python with pytximport thanks to
@compmed.bsky.social
et al.
academic.oup.com/bioinformati...
loading . . .
Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python
AbstractSummary. Transcript quantification tools efficiently map bulk RNA sequencing reads to reference transcriptomes. However, their output consists of t
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae700/7905459?searchresult=1
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reposted by
Nico Kaiser
Malte Kuehl
12 months ago
Thanks for sharing! Looking forward to see what more options to use data from kallisto & others with scientific python and
@scverse.bsky.social
ecosystem tools will enable
add a skeleton here at some point
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