Peter Kerpedjiev
@pkerpedjiev.bsky.social
Reposted by Peter Kerpedjiev
I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable".
Learn more at: oxbow.readthedocs.io
Learn more at: oxbow.readthedocs.io
July 7, 2025 at 9:22 PM
I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable".
Learn more at: oxbow.readthedocs.io
Learn more at: oxbow.readthedocs.io
New higlass-pileup update lets you sort reads by base! Available for use directly in a Juptyer notebook thanks to @manzt.sh. See docs for an example of how to use it:
docs-python.higlass.io/examples.htm...
docs-python.higlass.io/examples.htm...
February 3, 2025 at 4:32 PM
New higlass-pileup update lets you sort reads by base! Available for use directly in a Juptyer notebook thanks to @manzt.sh. See docs for an example of how to use it:
docs-python.higlass.io/examples.htm...
docs-python.higlass.io/examples.htm...
Reposted by Peter Kerpedjiev
Released juv v0.3.0! 🎉
Brings uv's locking for standalone scripts to Jupyter notebooks. Lockfiles are embedded directly in metadata for self-contained, reproducible notebooks.
- `juv lock` generates a lockfile
- `juv tree` shows dependencies
- `juv export` outputs pip-compatible format
Brings uv's locking for standalone scripts to Jupyter notebooks. Lockfiles are embedded directly in metadata for self-contained, reproducible notebooks.
- `juv lock` generates a lockfile
- `juv tree` shows dependencies
- `juv export` outputs pip-compatible format
![printing out a lockfile in the terminal for a Jupyter notebook. Terminal command: cat Untitled.ipynb | jq -r '.metadata["uv.lock"]' | bat -l toml](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:lf6ut5voripflo7pbdx6fyzh/bafkreigemr4xwlohjvjvchryzwcuq5mm3unhuxs5vt5jeov53lkzmxef2q@jpeg)
January 15, 2025 at 6:34 PM
Released juv v0.3.0! 🎉
Brings uv's locking for standalone scripts to Jupyter notebooks. Lockfiles are embedded directly in metadata for self-contained, reproducible notebooks.
- `juv lock` generates a lockfile
- `juv tree` shows dependencies
- `juv export` outputs pip-compatible format
Brings uv's locking for standalone scripts to Jupyter notebooks. Lockfiles are embedded directly in metadata for self-contained, reproducible notebooks.
- `juv lock` generates a lockfile
- `juv tree` shows dependencies
- `juv export` outputs pip-compatible format
Reposted by Peter Kerpedjiev
Pileup support is shaping up to be both performant and beautiful thanks to the Rust powered Oxbow package:
github.com/abdenlab/oxb...
Big shout out to @nvictus.bsky.social and @manzt.sh for implementing key features like buffering and file-like pointer support!
github.com/abdenlab/oxb...
Big shout out to @nvictus.bsky.social and @manzt.sh for implementing key features like buffering and file-like pointer support!
December 19, 2024 at 6:36 AM
Pileup support is shaping up to be both performant and beautiful thanks to the Rust powered Oxbow package:
github.com/abdenlab/oxb...
Big shout out to @nvictus.bsky.social and @manzt.sh for implementing key features like buffering and file-like pointer support!
github.com/abdenlab/oxb...
Big shout out to @nvictus.bsky.social and @manzt.sh for implementing key features like buffering and file-like pointer support!
Reposted by Peter Kerpedjiev
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
November 18, 2024 at 6:22 PM
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
Reposted by Peter Kerpedjiev
www.cell.com/cell/fulltex...
The chromosome folding problem and how cells solve it
Great review by @jobdekker.bsky.social & Leonid Mirny
The chromosome folding problem and how cells solve it
Great review by @jobdekker.bsky.social & Leonid Mirny
The chromosome folding problem and how cells solve it
All cells must fold their chromosomes. The combined action of a small set of conserved
molecular and biophysical mechanisms fold chromosomes in a variety of ways across
the cell cycle and tree of life...
www.cell.com
November 16, 2024 at 2:40 AM
www.cell.com/cell/fulltex...
The chromosome folding problem and how cells solve it
Great review by @jobdekker.bsky.social & Leonid Mirny
The chromosome folding problem and how cells solve it
Great review by @jobdekker.bsky.social & Leonid Mirny
Reposted by Peter Kerpedjiev
Big update over the weekend: datasets can now be organized into folders!
Also, the default ordering for projects is by the last time they were opened. Soon to come is an option to select how they are ordered.
Also, the default ordering for projects is by the last time they were opened. Soon to come is an option to select how they are ordered.
November 11, 2024 at 6:32 AM
Big update over the weekend: datasets can now be organized into folders!
Also, the default ordering for projects is by the last time they were opened. Soon to come is an option to select how they are ordered.
Also, the default ordering for projects is by the last time they were opened. Soon to come is an option to select how they are ordered.