Siva
@sivarajank.bsky.social
He/him, Bioinformatician @ imb.de
Opinions are my own
Opinions are my own
Reposted by Siva
Ah, here it is.
bsky.app/profile/sara...
bsky.app/profile/sara...
I was loving Claude Code... until I tried it with #rstats. Constant errors, wouldn't use the tidyverse even when asked, "optimized" functions were slower.
Frustrated, I started a session just to teach R to Claude and summarize what it learned into a CLAUDE.md file gist.github.com/sj-io/3828d6...
Frustrated, I started a session just to teach R to Claude and summarize what it learned into a CLAUDE.md file gist.github.com/sj-io/3828d6...
Claude R Tidyverse Expert
Claude R Tidyverse Expert. GitHub Gist: instantly share code, notes, and snippets.
gist.github.com
November 15, 2025 at 4:28 PM
Ah, here it is.
bsky.app/profile/sara...
bsky.app/profile/sara...
Reposted by Siva
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 22, 2025 at 12:38 PM
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!
Interested in learning about the single cell advances? Tune in to this event from SatijaLab. satijalab.org/scgd #SingleCell 🧬🖥️
/scgd25/
satijalab.org
March 9, 2025 at 10:17 AM
Interested in learning about the single cell advances? Tune in to this event from SatijaLab. satijalab.org/scgd #SingleCell 🧬🖥️
Reposted by Siva
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
January 3, 2025 at 7:25 PM
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
Reposted by Siva
🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41...
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
December 18, 2024 at 10:19 PM
🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41...
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
Reposted by Siva
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools. #GeneExpression #SingleCell #scRNAseq #NAR 🧬 🖥️
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools
Abstract. Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integ
academic.oup.com
December 7, 2024 at 11:20 AM
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools. #GeneExpression #SingleCell #scRNAseq #NAR 🧬 🖥️
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Siva
Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment https://www.biorxiv.org/content/10.1101/2024.11.27.625771v1
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment https://www.biorxiv.org/content/10.1101/2024.11.27.625771v1
Ultrafast mapping of short reads to transcriptomic and metagenomic references via lightweight mappin
www.biorxiv.org
December 2, 2024 at 11:25 PM
Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/
Reposted by Siva
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
Reposted by Siva
There’s an open postdoc position in our EIC funded project FIBRE-MATCH at the University of Helsinki, Finland. Further information in the ad.
jobs.helsinki.fi/job-invite/3...
jobs.helsinki.fi/job-invite/3...
Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome
Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome
jobs.helsinki.fi
November 19, 2024 at 3:12 PM
There’s an open postdoc position in our EIC funded project FIBRE-MATCH at the University of Helsinki, Finland. Further information in the ad.
jobs.helsinki.fi/job-invite/3...
jobs.helsinki.fi/job-invite/3...
That's a cool and trendy way to advertise
Explore our matchmaking portfolio in which you can browse SciLifeLab Group Leaders and find the perfect host for your project ↓ 🧪🌍🖥️🧬
www.scilifelab.se/research/pul...
#AcademicSky #MolBiol #AcademicSky
www.scilifelab.se/research/pul...
#AcademicSky #MolBiol #AcademicSky
Pulse - Application
Application PULSE postdoc applicants have the opportunity to choose between an academic or an entrepreneurial track. Both fellowship tracks will include advanced training in research and transferable ...
www.scilifelab.se
November 28, 2024 at 7:13 AM
That's a cool and trendy way to advertise
Reposted by Siva
New work reveals the impact of anxiety & depression on PhD students.
"Anxiety and depression can have a substantially detrimental impact on graduate students’ experiences [..] and likely also contribute to increased time to degree and student attrition."
nature.com/articles/s41...
"Anxiety and depression can have a substantially detrimental impact on graduate students’ experiences [..] and likely also contribute to increased time to degree and student attrition."
nature.com/articles/s41...
November 27, 2024 at 4:14 AM
New work reveals the impact of anxiety & depression on PhD students.
"Anxiety and depression can have a substantially detrimental impact on graduate students’ experiences [..] and likely also contribute to increased time to degree and student attrition."
nature.com/articles/s41...
"Anxiety and depression can have a substantially detrimental impact on graduate students’ experiences [..] and likely also contribute to increased time to degree and student attrition."
nature.com/articles/s41...
Reposted by Siva
I created a starter pack including people working in #bioinformatics core facilities 🧬 🖥️
I am sure I missed a lot of relevant people, so if you'd like to be added or know people who should be in there, let me know!
go.bsky.app/LfGCpSX
I am sure I missed a lot of relevant people, so if you'd like to be added or know people who should be in there, let me know!
go.bsky.app/LfGCpSX
November 26, 2024 at 9:30 AM
I created a starter pack including people working in #bioinformatics core facilities 🧬 🖥️
I am sure I missed a lot of relevant people, so if you'd like to be added or know people who should be in there, let me know!
go.bsky.app/LfGCpSX
I am sure I missed a lot of relevant people, so if you'd like to be added or know people who should be in there, let me know!
go.bsky.app/LfGCpSX
I was forced to think about a friendlier color scheme during the revision of my first paper.
Perhaps, the journals should start emphasizing on adapting color blind friendly color schemes.
Perhaps, the journals should start emphasizing on adapting color blind friendly color schemes.
Always run your color schemes through software to check this. It's easy. Also... just don't ever use default color schemes? ✌️
(btw, this example is the gglot default color scheme, so even worse than just in #SingleCell, it applies to wide swatches of data sci)
(btw, this example is the gglot default color scheme, so even worse than just in #SingleCell, it applies to wide swatches of data sci)
(please amplify) 4% of scientists face an important barrier to an the ENTIRE FIELD of single-cell genomics and here is why
November 26, 2024 at 3:02 PM
I was forced to think about a friendlier color scheme during the revision of my first paper.
Perhaps, the journals should start emphasizing on adapting color blind friendly color schemes.
Perhaps, the journals should start emphasizing on adapting color blind friendly color schemes.
Reposted by Siva
For nearly 20 years, I've posted all my teaching slides & materials on my dedicated teaching website
Do check it out!
If you want to use anything, no need to ask for permission - just use with credit!
www.teachepi.org
Do check it out!
If you want to use anything, no need to ask for permission - just use with credit!
www.teachepi.org
November 24, 2024 at 4:03 PM
For nearly 20 years, I've posted all my teaching slides & materials on my dedicated teaching website
Do check it out!
If you want to use anything, no need to ask for permission - just use with credit!
www.teachepi.org
Do check it out!
If you want to use anything, no need to ask for permission - just use with credit!
www.teachepi.org
Reposted by Siva
My panel in London this week on accelerating science with A.I.
@deep-mind.bsky.social
www.youtube.com/watch?v=QK_U...
@deep-mind.bsky.social
www.youtube.com/watch?v=QK_U...
Science in the Age of AI | AI for Science Forum
YouTube video by Google DeepMind
www.youtube.com
November 21, 2024 at 4:14 PM
My panel in London this week on accelerating science with A.I.
@deep-mind.bsky.social
www.youtube.com/watch?v=QK_U...
@deep-mind.bsky.social
www.youtube.com/watch?v=QK_U...
Reposted by Siva
A big day of output for the Human Cell Atlas, a global collaborative project with 100 countries to understand our ~37 trillion cells
A Wikipedia of our cells, a "remarkable achievement"
nature.com/articles/d41...
nature.com/immersive/d4...
A Wikipedia of our cells, a "remarkable achievement"
nature.com/articles/d41...
nature.com/immersive/d4...
November 20, 2024 at 5:04 PM
A big day of output for the Human Cell Atlas, a global collaborative project with 100 countries to understand our ~37 trillion cells
A Wikipedia of our cells, a "remarkable achievement"
nature.com/articles/d41...
nature.com/immersive/d4...
A Wikipedia of our cells, a "remarkable achievement"
nature.com/articles/d41...
nature.com/immersive/d4...